If you stop to think about it a bit, you'll realize that Hindus are in a weird place. They're an ancient religion, old as or older than just about every other pantheon portrayed in this game. This, as well as the fact that they are a polytheistic religious tradition means they get lumped in with ancient Greek, Egyptian, and Norse faiths. The problem is that, revival movements aside, Hinduism is still a major world religion. The others are not. There are still millions of practicing Hindus. Hellenismos, Kemetism, Asatru, and other 'neopagan' faiths are still tiny (and, it must be said, fully aware of how their religious figures have been adopted by pop culture. They generally go into the practice expecting this sort of thing.)
Not a lot of people get worked up over portrayals of Thor or Anubis because not many people still hold these figures in reverence. Hindus are going to be as sensitive as Christians and Muslims when it comes to their gods. The devs should probably have asked themselves, 'If we could justify it from a gameplay perspective, would we have put Jesus or Mohammed in the game?' If sensitivity to religion was a factor in the decision not to, they should have applied that same sensitivity to Hinduism.
This isn't to say that I thin PAX should cave, nor should the developers of the game. They are free to make the game they choose, play the game they choose, and let consumers decide whether what they have is worth anything. However, that shouldn't prevent us from attempting to gain some understanding of the people involved. It's possible to sympathize with both sides, no matter who you agree with. I think that Hindus should probably just let this go and go on with their lives. But then again, I'm not a Hindu.