When in the year 2030 IS takes over the world, the Pope escapes justice by going back in time with a hit list that can prevent all future holy wars.

I think both those logline tries add a new element, (That the pope is just a puppet) without really increasing the word count. Both would work.

Yes, this logline is more to the point. How about this:

"When IS conquers the world, a conclave of cardinals send a puppet Pope back in time to assassinate IS future leaders and prevent a religious catastrophe.?

or simply this:

When ISIS conquers the world, a puppet Pope must travel back in time to assassinate their future leaders and prevent a religious catastrophe.?

What do you think?

"When ISIS conquers the world, the Pope must travel back in time to assassinate their future leaders to prevent the coming religious catastrophe."