Yes. The degree will definitely be valid. The court order is to the universities regarding the name used but not about the degree awarding authority. So it shouldnt affect you at all.

Let me be more specific. Many of the leading private universities are "deemed to be universities" whcih means that they are like Universities unlike Delhi University, Calcutta University, Andhra University which were established as universities. However many of the private ones started as institutes and grew to apply for university like status which is the "Deemed to be University". Now all of them were asked by the court not to say university behind their name but specify deemed to be university after their name. Thats it. 

So it wont affect students and the degrees will definitely be valid. Pls dont worry on that account.