I agree with PP. My DH gets mad if I make any relatively important decision without him. Yours was a BIG one. And, by not talking with him about it beforehand, even if you ended up disagreeing with him, sent a pretty negative message to him, I'd think. It says that even though he is "the daddy" and has been for years and by your side and with your support, that you don't really think of him as an equal partner when it comes to your son. He may have had alot of issues with bio father coming into the picture, he may have had none. He may have been the voice of reason, made suggestions on ways to make it less traumatic for your for the process, slow you down so you could really interpret the situation from a different perspective (like drugs/jail other problems) that you may not have thought. But, you took that away from him, and even though you recognize that this could hurt him, I sounds from your post that you think it's the DS and bio father that hurts, and I think it's probably much more. Did you ever talk about what you would do if/when bio dad ever showed up?
Now, I'm not saying you weren't well intentioned or that you acted instinctively, or that you're evil or anything. But, I wanted you to think about this from another perspective.
How to make it better? I'd sit down with DH and start the conversation with "I messed up big time and I'm sorry." Tell him some of the stuff that you've been withholding from him (I'm assuming you withheld to save DH's feelings?) and why, explain that you just acted instinctively based on what was going on, that DS was sitting there, and you just allowed it. You didn't think, not really, and you have had time to think about it and you just feel terrible. Tell him you'd really like to talk about this with him and figure out what to do from here as a couple and as parents. In the discussion, one thing to consider is that as much as it's a potential mess for DS, DH and you, bio-dad does have legal rights to see his son, unless those were ever specifically revoked.
Big hugs, I can only imagine how hard this is for all of you!