I would imagine your DS is a bit stressed/worrying a bit about his exams, and really doesn't like your DD's boyfriend. It sounds like they clash (you said the bf is a bit rough and your DS is quite gentle, not really that type of person), which is fine, we obviously can't get on with everybody, but a bit unfortunate in this case.
He probably can't understand why DD wants to go out with somebody so horrible (in his opinion), and knowing it's serious (likely to have sex etc.) makes it seem even worse to him.
So between exams, that and probably his hormones too I would think it's all got a bit much for him and he's lashing out.
I think you've sorted out your DD for the moment (well done for that), so should probably focus on him now, even if it's just trying to make him forget about DD and her boyfriend. Would you be happy with them spending more time out together, at the cinema for example? Or going to his house a bit more? Just to keep them out of DS's way a little bit? I know he will have to deal with it at some point, but this time of year's probably hard enough for him without her adding to it!
He does need to get over it, but I think at the moment his revision should be the priority so don't go in heavy handed. 16 year olds aren't always as grown up as you'd think, and it sounds to me like he's struggling emotionally. Maybe he's not liking proof his little sister's growing up because he doesn't feel/want to be that grown up?
Perhaps have one go at explaining to him that if his DSis is going to have sex you all want her to be as safe as possible. Don't say you think she should/shouldn't, just say you want the best outcomes if she does. And then leave it.
And maybe give him a few treats (new highlighters for revision, or some chocolate) or take a drink and biscuit into him while he's working or give him hugs (if he'll let you!), just so he definitely knows you're there if he does want to chat about anything.