Srivaishnavite temples have Sudarshana Chakras that are worshiped. Is there a scriptural basis for that? Does any other sect worship the Sudarshana Chakra?
Yes, Lord Sudarshana is worshipped as deity. There are many scriptures mentioning it. Rickross has already answered from Agamas,I'm here adding from Agni Purana chapter 63:
एवं ताक्ष्यस्य चक्रस्य ब्रह्मणो नृहरेस्तथा।
प्रतिष्ठा विष्णुवत् कार्या स्वस्वमन्त्रेण तां श्रृणु ।। १ ।।
सुदर्शन महाचक्र शान्त दुष्टभयङ्कर।
च्छिन्द छिन्द भिन्द भिन्द विदारय विदारय ।।
परमन्त्रान् ग्रस ग्रस भक्षय भक्षय भूतान्
त्रासय त्रासय हूं फट सुदशनाय नमः ।।
अभ्यर्च्य चक्रं चानेन रणे दारयते रिपून् ।। २ ।।
The god said:
The installation [i.e., pratiṣṭhā] of the (images of) Garuḍa (vehicle of Viṣṇu) Brahman, Nṛhari (man-lion form of Viṣṇu) and of the (sudarśana) disc should be done in the same way as that of Viṣṇu with their respective mantras. Listen to me.
O Sudarśana! The great disc that is tranquil! Dreadful to the wicked! Kill kill, pierce pierce, cut through and cut through.
Devour devour the incantations of others. Eat up, eat up the evil spirits. Frighten frighten, huṃ phaṭ, salutation to sudarśana. Having worshipped the disc with this mantra one destroys the enemies in the battle.
If he is worshipped with mantra, it means he is deity.
Quoting from the PDF Pancharatra Prayoga (hosted by Sri Vaishnava site Srimatham.com):
Invocation of sudarśana
śaṅkhaṁ cakraṁ ca cāpaṁ paraśuṁ asimiśuṁ śūla pāśāṁ kuśāṁśca |
bibhrānam vajra keṭaṁ hala musula gadā kuṇṭaṁ atyugra daṁṣṭraṁ ||
jvālā keśaṁ trinetraṁ jvaladānala nibhaṁ hāra keyūra bhūṣam |
dhyāyet śaṭkona saṁsthaṁ sakala ripu-kula prāṇa saṁhāra cakram ||
I visualize Sudarshana the eliminator of all hostile forces, located within the six-‐‑cornered star, bearing the conch, discus, bow, axe, sword, trident, noose, goad, the diamond-‐‑shield, plough, cudgel, mace, spear, with aweful sharp fangs, with blazing halo, three eyes, the intensity of a raging inferno, adorned with garlands and anklets
Since Dhyana Mantra exists that means Sudarshana is a deity. The booklet then explains how to do Avahana of the deity and complete the worship:
oṁ sahasrāra huṁ phaṭ v Place flower and water on top of the kalaśa;
oṁ namaḥ sudarśanāya āgaccha āgaccha [3 times]
v offer āsanam then do nyāsa on the kalaśa. oṁ ācakrāya svāhā jñānāya namaḥ [heart ] oṁ vicakrāya balāya svāhā [head] oṁ sucakrāya vīryāya vaṣaṭ [sikhā] oṁ sūrya cakrāya svāhā aiśvaryāya huṁ [shoulders] oṁ jvāla-cakrāya svāhā tejase phaṭ [eyes ] oṁ mahā sudarśana cakrāya svāhā śaktyai vauṣaṭ. v snap finges around the kalaśa and show cakra mudra, dhenu mudra and yoni mudra
The mantra in bold is the Avahana Mantra used. Since the booklet is titled "Pancharatra Prayoga", presumably the details are taken Vaishnava Pancharatra texts.