Should I tell her something like "I think we should stop having sex"? What if she asks "Why?" in response?
Q: If you were in her shoes, how would this come across? A: You would think she is weak as [censored].
As SteveLW says, women can’t be in a healthy relationship with men they don’t respect.
Don’t go out of your way to tell her anything. But next time she tries to initiate sex, say “I don’t want sex with someone who is having an affair.” Make sure it’s a stark, clear boundary but don’t dwell on it or get pulled into a discussion. Immediately end the discussion, or even go to sleep/go out.
She might be enjoying sex with you physically atm, but she has zero respect for you because you’re willing to do that in the knowledge she’s with someone else.
And don’t do this to punish her or teach her a lesson… do it because you have self respect and boundaries.