In that case, the junior partner would become independent. But that is not because of religion, it is because PU members always become independent if the senior partner is annexed.
However, if you vassalized the senior partner then you would take over the PU and it doesn't matter whether you are Christian or not.
There is nothing in the game that forbids non-Christians to lead a PU, it's just a very unlikely thing to happen because they cannot marry Christians. But if they somehow manage to acquire a PU by other means, it is perfectly valid.