I thought I remembered them having sex next to someone's dead body but I didn't recall it being rape. Which, I agree completely, felt really out of place for Jaime's character in the show.

I don't recall Dontos being killed either, I was questioning that as well. I do seem to recall the "pay a man and he'll keep quiet for a time, kill a man and he'll keep quiet forever" line though. Littlefinger has always been self-serving. This does make that a bit more blatantly obvious. One thing I do think it works for is establishing a reason for why Sansa should do what he says when they get to the Eyrie.

The shackles in the barrels was pure genius.