I assume the Pakistani Air Defence system relies on ground based radar. In that case a couple of non squawking helicopters would be very difficult to detect. Especially if you are looking further afield and do not (in a million years) expect that kind of attack.
The jets were probably scrambled after word came through of an attack in progress, rather than radar hits. This would be nothing more than an escalation of alert states in case this signalled the start of someting bigger.
As to being engaged by US jets. Bringing down a Pakistani jet over it's own sovereign territory woud have opened up a whole can of worms. That said, I doubt the Americans would be bothered when you consider the prize.
IMHO