How upsetting for you endoxana.
I think the danger of not calling him on his threat of divorce is where does that end?
Even if it is an empty threat on his part, it obviously doesn't feel that way to you and genuinely scares you. If he sees that it works then what's to stop him using it on other occasions where he wants to get his own way?
The problem with his attitude is that this is already a compromise with regards to the name. For example, you would be perfectly within your rights to suggest DS2 takes your surname, especially as DS1 already has his fathers (not traditional, but still totally within your rights!). Therefore, DS2 taking your maiden name as a middle name is already a compromise on your behalf. DH gets to pass on his family name to future generations but you do not, so the least DH can do is agree to your maiden name as a middle name. He won't see it this way obviously, but that's how it is. It is absolutely no skin off his nose if DS2 has your maiden name as a middle name, it doesn't affect him in the slightest. Therefore this is very controlling behaviour IMO. And why does he get the final word on this? Because he is threatening you.
You would have to be very strong indeed to call him on this bluff, and because of the circumstances and how vulnerable you probably are at the moment it is absolutely fair enough if you don't want to. However, I think at some point in the future, even if you submit this time, I'm sure this threat will come up again (especially if it works this time).
I think you need to consider the implications (practical, financial, emotional) of calling him on his threat (again, not necessarily now). I have to say that I think only when you are actually prepared to divorce him will you be able to stand up to him and possibly get him to back down. The only way to disarm him and stop him holding all the power is to accept the consequences of his threat. Hopefully, if he relises you are serious this might be enough to get him to back down. But if not, and he really would divorce you over this, is that really someone you want to be married to? Is his son having your maiden name as a middle name so terrible for him that he couldn't be married to you any more?
I also think that this is the time (after having a baby) that DH should be going out of his way to support you, not threatening you with divorce because you have the audacity to question his completely unfair unilateral decision.
I'm so sorry you are having to deal with this at what should be a lovely, happy family, supportive time. Its very, very unfair.