They didn't have sex next to a body at all; they had sex in the sept when Cersei was on her period, and she does sort-of-kind-of resist at first but clearly changes her mind. The scene in the TV show got it wrong, in my opinion, and very clearly was rape - a bad choice, since it really dehumanizes Jaime at the wrong time.
That happened much the same, but if I recall correctly it was Petyr himself who pulled the trigger. Littlefinger is VERY CLEARLY a bad guy in the books by that point.
The good news is, they won't have her really doing nothiung for too long. They'll either put some extra stuff in, or just go away from that storyline for a bit.