It is not necessary for any pillion to ride side saddle in Iran or Pakistan or even India for that matter. The fact that some locals do is more of a cultural thing. I've seen local women pillions in Iran riding normally.
As for an Indian getting a visa for Pakistan, this should be possible but relations between the two countries are variable to say the least. I can only advise keeping up with the news and asking the advice of the Pakistani Consulate now and then once more about 3-4 months before you intend to leave. You should then know what type of visa can be issued, how long it would be permitted to stay in Pakistan and how long the visa would be valid for. When I went there I was given a 45 day visa valid for 6 months but I'm a UK citizen and an Indian is unlikely to get the same deal.