I love these kinds of questions because they give an opportunity to meta-analyze and bring out deeper insights into our heritage.
You have only looked at the first part of the story. Besides, you are missing the various levels of symbolism by reducing it to a mere human-level event of biological reality, which if you haven't realized as an implausibility, is only pitiable as being naive. I can say in return that I find this reduction to a social justice issue very vulgar and "disgusting" as well.
This story occurs in Adi Parva chapters 24-25. Verses 10-14 of chapter 24 narrate Garuda eating the Nishadas. However, in chapter 25:
तस्य कण्ठमनुप्राप्तो ब्राह्मणः सह भार्यया । दहन्दीप्त इवाङ्गारस्तमुवाचान्तरिक्षगः ॥ १
As he was swallowing, a Brahmana and his wife also reached his throat. Feeling a burning as like a burning piece of coal, Garuda addressed the Brahmana. (1)
द्विजोत्तम विनिर्गच्छ तूर्णमास्यादपावृतात् । न हि मे ब्राह्मणो वध्यः पापेष्वपि रतः सदा ॥ २
O Brahmana, please come out quickly through my open mouth. I am not supposed to kill a Brahmana even if he is always engaged in sin. (2)
ब्रुवाणमेवं गरुडं ब्राह्मणः समभाषत । निषादी मम भार्येयं निर्गच्छतु मया सह ॥ ३
Having been addressed thus by Garuda, the Brahmana replied, let my wife, a Nishadi, also get out with me.
एतामपि निषादीं त्वां परिगृह्याशु निष्पत । तूर्णं संभावयात्मानमजीर्णं मम तेजसा ॥ ४
Gathering up the Nishadi also, quickly jump out, so that you will be saved from being digested by my energy.
ततः स विप्रो निष्क्रान्तो निषादीसहितस्तदा । वर्धयित्वा च गरुडमिष्टं देशं जगाम ह ॥ ५
Then, the Brahmana got out along with his Nishadi wife. Having blessed Garuda, he went his way.
However, later in verse 8 Garuda says he's still not full after eating thousands of Nishadas. This itself should suggest the mythical nature of the story:
मात्रा चास्मि समादिष्टो निषादान्भक्षयेति वै । न च मे तृप्तिरभवद्भक्षयित्वा सहस्रशः ॥८
I was advised by my mother to eat Nishadas, but I'm still hungry after eating thousands of them.
He asks his father to tell him what else he can eat to feel full and to give him the strength to get the Amrita:
तस्माद्भोक्तव्यमपरं भगवन्प्रदिशस्व मे । यद्भुक्त्वामृतमाहर्तुं समर्थः स्यामहं प्रभो ॥९
Hence, please direct me to something I can eat, by which I can have the strength to get the Amrtam.
Kashyapa tells him about 2 great Maharshis who were brothers, and who were disputing their share of their inheritance. And through disagreements, they curse each other to become transformed into an elephant and a tortoise, and they continue to keep fighting each other.
आसीद्विभावसुर्नाम महर्षिः कोपनो भृशं । भ्राता तस्यानुजश्चासीत्सुप्रतीको महातपाः ॥१०
There was a Maharshi named Vibhavasu, very short-tempered by nature. He had a brother named Supratika, who was also a great sage.
After they have long arguments, the elder brother curses the younger brother:
नियन्तुं न हि शक्यस्त्वं भेदतो धनमिच्छसि । यस्मात्तस्मात्सुप्रतीक हस्तित्वं समवाप्स्यसि ॥१६
You are completely out of control, and you want to force a split in the inheritance. Because of that, you will become an elephant.
शप्तस्त्वेवं सुप्रतीको विभावसुमथाब्रवीत् । त्वमप्यन्तर्जलचरः कच्छपः संभविष्यसि ॥१७
Having been cursed, Supratika cursed his brother as well, saying 'you will also become a tortoise'.
एवमन्योन्यशापात्तौ सुप्रतीकविभावसू । गजकच्छपतां प्राप्तावर्थार्थं मूढचेतसौ ॥१८
Thus having cursed each other, they became an elephant and a tortoise, due to fights over money, the fools.
Anyway, long story short, the elephant and tortoise are both gigantic, and they clash with each other at every opportunity. Kashyapa tells Garuda to eat them.
तावेतौ युद्धसंमत्तौ परस्परजयैषिणौ । उपयुज्याशु कर्मेदं साधयेप्सितमात्मनः ॥२५
Eat these two who are always fighting each other, and accomplish your goal.
So the following points are noteworthy:
Obviously this story is mythical in nature, and it is inappropriate to blow it out of proportion by injecting all kinds of social injustice theories. This is analogous to saying that depicting Asuras as the "bad ones" and having Devas "massacre" them is "disgusting" and is social injustice to them. There are all sorts of characters in creation, and some are closer to settled culture, and some are still farther away. So from the point of view of settled culture, the ones that stand at a distance from it are abhorrent. This is seen in all cultures of the world. Any group that is on the periphery of the cultural circle is labeled as "barbarian" or other name. SJW activism incorporates the greatest amount of hypocrisy within itself, because it is entirely sustained on the tolerance of a cultured society which can take criticism, while the SJW activism itself cannot venture outside the ambit of culture and civilized society. Ideas of rendered injustice themselves find definition and meaning within a law-governed and cultured refined society. Outlaws do not tolerate SJWs. This itself limits the purview of social injustice theories and activism.
Even if we stoop down to the level of human affairs, the reality of civilized societies throughout history is that there have always been groups that have been outside of the circle of civilization and settled life who have been a threat to it. Culture brings gentleness and reduces the ferocity of a wilder existence, and the ferocious always prey upon the gentle. So this above story may reflect those ancient times when frequent interaction between settled society and non-settled elements may have occurred, and the latter may have been viewed as threats.
Even if it is taken as a statement of some social injustice or discrimination against Nishadas, it is evident that a Brahmana could marry a Nishada without anyone raising an eyebrow, and there was true love which overcame any caste injustice allegations. The Brahmana did not abandon his Nishada wife through the life-threatening situation. He saved her as well.
Further, still at the level of human affairs, the story clearly shows that Garuda even eats Brahmanas who are great sages, who are not behaving as they should. So at a social justice level, even Brahmanas are not spared.
Going back up to a higher level of symbolism and myth, if your allegation of "genocide" of Nishadas was a constant theme in Itihasas and Puranas, then there wouldn't have been the story of Vena in Bhagavata Purana and Vishnu Purana. Vena who is a wicked king, is killed by a group of sages, and they rub the thigh of the dead body, from which Nishada is born. And then the Nishada becomes the originator of his people and rules over his own kingdom. If our tradition wanted to "kill off" the Nishadas, why even invent an origin story for them? Why even have them exist, thrive, prosper in their own kingdom? The answer to this is found at a much higher level of philosophy than at the lower level of human affairs. The universe exists only because there is constant localized imbalance between the three gunas Sattva, Rajas and Tamas. When the three come into equilibrium, then Pralaya (dissolution) occurs. But in the meantime, the three gunas are interacting with each other, and they are constantly disappearing and reappearing locally. So if the universe exists, it is proof that the three gunas are constantly battling each other in a tug-of-war situation. This is why while some Nishadas are getting eaten, others are still thriving and prosperous. This is why while the Maharshis are eaten, other Brahmanas are thriving. This is why while Vena the bad Kshatriya is killed, another good Kshatriya Prthu is born. The gunas are not manifest based on caste, they are spread across all castes.
There is another level of poetic symbolism, called Dhvani (subtle suggestion). The Dhvani is clearly seen in the verse 2 of chapter 25, where Garuda is made to say that he cannot kill a Brahmana even if he is always engaged in sin. The subtle suggestion here is that Garuda himself is not fully convinced about this rule that Brahmanas are above everyone else. The follow-up of this Dhvani is seen in the subsequent story of the fighting Maharshis who are eaten by Garuda, hence proving his own doubt about the infallibility of Brahmanas.
EDIT: I just hit upon another idea/symbolism regarding why Garuda was asked to eat Nishadas. Now, Nishadas are hunters, but primarily bird hunters. So this could be a symbolism for a balance of actions. Garuda, as the king of birds is taking "revenge" on the Nishadas for killing thousands of birds. This is evidenced by Valmiki's shloka:
मा निषाद प्रतिष्ठां त्वमगमः शाश्वतीः समाः । यत्क्रौञ्चमिथुनादेकमवधीः काममोहितम् ॥
Oh Nishada, may you never have peace, as you have killed one of the Krauncha pair of birds engaged in copulation.