It is said that Mind is simply a bundle of thoughts and the patanajali yoga sutras says "yogachittavritiinirodha". Since the thought process is restrained through meditation and ego is dissolved,veil of ignorance ceases and self is realised.. So, What is there to unite? as Yoga means union of individual and supreme self.
The union of Atma and Paramatma is called Yoga which you have already stated. Such a definition is found in several scriptures.
From Devi Bhagavatam 7.35 for example:
- Himâlayâ said :-- "O Mahes'varî! Now tell me the Yoga with all its Amgas (limbs) giving the knowledge of the Supreme Consciousness so that, I may realise my Self, when I practise according to those instructions. 2-10. S'rî Devî said :-- "The Yoga does not exist in the Heavens; nor does it exist on earth or in the nether regions (Pâtâla). Those who are skilled in the Yogas say that the realisation of the identity between the Jivâtma and the Paramâtmâ is "Yoga." O Sinless One! The enemies to this Yoga are six; and they are lust, anger, greed, ignorance, vanity and jealousy
And to achieve that union, the mind, which is nothing but the sixth Indirya, has to be dissolved.
To understand this we need to understand a process called Bhutasuddhi given in several Tantras.
First, we need to understand how the evolution of Parabrahaman has resulted in the creation.
And then in Bhutasuddhi we imagine an involution where the various aspects and Tattvas of body are dissolved into the source from where it came.
So, the lower Tattvas gradually get dissolved into the higher Tattvas and so on until the highest Tattva is reached. Since mind is not the highest Tattva it will be dissolved somewhere in between into the Tattva it came from.
So, basically in Bhutasuddhi we reverse the process of creation.
Therefore, we have something like this (in the words of Arthur Avalon):
Earth is associated with the sense of smell, water, with taste, fire, with sight, air, with touch, and ether, with sound. Kundalini is roused, and led to the svadhishthana Chakra. The "earth" element is dissolved by that of "water," as "water" is by "fire," "fire" by "air," and "air" by "ether." This is absorbed by a higher emanation, and that by a higher, and so on, until the Source of all is reached.
And when this source of all is reached that is when the union of Atma and Paramatma has been achieved and to attain that mind has to be dissolved somewhere in between. Because mind is nothing but the product of the Tattvas and is a part of the larger Antahkarana.
O Girijâ! Each of the five original elements is divided into two parts; one part of each of which is subdivided into four parts. This fourth part of each is united with the half of four other elements different from it and thus each gross element is formed. By these five gross elements, the Cosmic (Virât) body is formed and this is called the Gross Body of the God. Jñânendriyas (the organs of knowledge) arise from Sattva Gunas of each of these five elements. Again the Sattva Gunas of each of the Jñânendriyas united become the Antah Karanâni. This Antah karana is of four kinds, according as its functions vary. When it is engaged in forming Sankalpas, resolves, and Vikalpas (doubts) it is called "mind." When it is free from doubts and when it arrives at the decisive conclusion, it is called "Chitta"; and when it rests simply on itself in the shape of the feeling "I", it is called Ahamkâra.
Devi Bhagavatam 7.31
The process of this involution (or Bhutasuddhi) is given by Lord Sadashiva in Mahanirvana Tantram's Chapter 5 and is as follows:
Then in the following manner let him fence all the quarters so that no obstructions proceed from them. Join the first and second fingers of the right hand, and tap the palm of the left hand three times, each time after the first with greater force, thus making a loud sound, and then snap the fingers while uttering the weapon-Mantra (92). He should then proceed to perform the purification of the elements of his body. The excellent disciple should place his hands in his lap with the palms upwards, and fixing his mind on the Muladhara Chakra let him rouse Kundalini by uttering the Vija "Hung." Having so roused Her, let him lead Her with Prithivi by means of the Hangsa Mantra to the Svadhishthana Chakra, and let him there dissolve each one of the elements of the body by means of another of such elements (93-94). Then let him dissolve Prithivi together with odour, as also the organ of smell, into water. Dissolve water and taste, as also the sense of taste itself, into Fire (95). Dissolve Fire and vision and form, and the sense of sight itself, into air (96). Let air and touch, as also the sense of touch itself, be dissolved into ether. Dissolve ether and sound into the conscious Self and the Self into Mahat, Mahat itself into Prakriti, and Prakriti Herself into Brahman (97)
So, without the mind being dissolved reaching the highest source (which is the goal of Yoga) isn't possible.
Therefore, between Yoga being so named and the fact that in Yoga the mind dissolves there is no contradiction at all.