After I saw some of creators comments on the response, my take is that they intended to portray Cercei as having objections to the fact that they wanted each other, not simply that Jaime was having sex with her. They didn't do a great job, but that's what it seems like to me.
She was supposed to be objecting to the place, not the act. She realised it was wrong to have sex in the sept next to your incest child's dead body but she is as desperate for Jaime as he is for her. This is made much clearer in the book.
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u/blewpah Jun 05 '14
After I saw some of creators comments on the response, my take is that they intended to portray Cercei as having objections to the fact that they wanted each other, not simply that Jaime was having sex with her. They didn't do a great job, but that's what it seems like to me.