I don't think Pakistanis nor Indians (for the most part) ever had that in mind. There are many Muslims in India (more than the population of Pakistan apparently) and there are also many Hindus in Pakistan. (I use Islam and Hinduism in this comparison as they are the two most followed religions in each of their respective countries).
While religion isn't a huge deal for most cricket lovers, it's certainly a huge deal for a sizable portion of the population. I know for a fact, from personal experience, that many Muslims in Mumbai will support Pakistan in an India-Pakistan game. It's simply because they feel like they can identify with the team better.
That said, religion doesn't really play that huge a part on a higher level. I remember at the conclusion of the 2003 World Cup, some idiot religious leader in India proclaimed that it was a "victory of hinduism". It was quickly pointed out that at least half the squad and several of the match-winners were Islamic. He shut up pretty quickly.