Just because they are separated, all is not lost. I have seen God restore many marriages. I would be supportive of him, dont tell him to leave her, let that be his decision and be an ear when he needs to talk. He is going to grieve this marriage just like one would a death.

If they have kids and there are no glaring issues such as drug abuse or infidelity, maybe you can encourage him to seek marital therapy. I think its a shame that people just throw away marriages without exhausting all efforts to try to save them. I am not speaking about your sons situation, but just in general. Good luck.