Maybe the therapist suggested couples therapy knowing full well the suggestion alone is godawful in order to get OP to unwittingly confront him about him not caring about OPs feelings and wellbeing. She(?), like PPs, is probably struggling to reach OP with the truth and is simply being pragmatic in order to maintain rapport in a situation where keeping channels of communication open is better than making OP stop going.
Pragmatism is one thing, though, malpractice another, and no therapist should ever suggest that to a rape victim.
OP wishes the rapes wouldn't bother her (but they obviously do), what does bother her is his "moods", ie his aggression and strong disregard of his children crying because they feel scared.
Do your children cry when you're hoovering OP?
He obviously uses the hoovering to scare your children so that you "do your job" and spring into action.
It's not that he has a couple weaknesses offset by his disney dad persona and wonderful performance as the family protector and patriarch OP - it's all part of his manipulation of you and the kids to keep you all in line. It's an oppressive system of intermittent reward, not a personality flaw or short-lived stressy situation.
ETA: You may think you would take from your children their great dad, but you would also give them back their mother, one that is no longer abused. And he would still be their dad after a separation, you wouldn't be taking anything from them. A separation could give them back their childhood, though. Doubtful they will look back on theirs with the angry hoovering, walking on eggshells and mother being scared in the mix.