The constitution of India doesn't explicitly talk about the freedom to enter India, it does however grant freedom of movement inside India with some reasonable restrictions (it is ironically not clearly defined as to what may be reasonable). Now it may be argued that for someone to be able to exercise their rights to this freedom, they must be allowed to enter India in the first place, denying entry into India does in fact deny people of this constitutionally guaranteed freedom.
In my opinion, the governments decision to restrict travel into the country for its own citizens is illegal, however for the legality to be determined this order needs to be challenged before a court of law. And as things currently stand most courts in India are currently closed (due to the COVID-19 pandemic) and those that are open are only conducting essential business (essential business again isn't very well defined).
Now as a matter of practice, if you were to show up at a land border or arrive in India by private boat it is highly unlikely that you will be denied entry into the country. The issue really is arriving by air and what happens is that the government issues a directive to the airlines telling them that they are not to allow passengers to board. So technically it is the airlines that is denying people boarding and also note that the ban isn't absolute, you can connect with an Indian mission and in extenuating circumstances they will provide you with documentation that will allow you to travel to the country.
Once this pandemic passes, it will be interesting to see if someone brings this up before a court; however it is unlikely that it will be of any benefit to people who got stuck in limbo this time around.