I could be wrong, but I had the feeling that the Clark/Elizabeth assignation wasn't taking place in their own home, but in a motel room somewhere, which they had rented for the purpose of the role-playing. It just didn't look like their home or their bedroom to me.
Now, just so I can get clear on something: So, Claudia had an affair with someone, and then blew her cover (which, actually, is pretty unbelievable to me--not the affair, but that she'd blow her cover). How did that lead to the murder of the agents? In addition to blowing her own cover, did she (unbelievably) also tell this lover the identity of all her sleeper agents? Why would she do that? And does this revelation clear up who did the murders? Like, can we conclude that it must be America, because there's no cover to blow as far as the Centre is concerned?