It is sad, in my opinion, that this is even a question. There is no reason that Pakistan and India have to be deadly enemies. Your two countries' cricket teams play each other and so do your hockey team. You are not at war with each other (even with the situation in Kashmir).
Surely if there were more marriages and other contacts between the two countries, things would be better. So to me it might be a good thing if they marry.
But that should all be irrelevant anyway. People should do what they want in terms of marriage -- it's love, not a political statement.