I think McBain feels guilty because he is partly responsible for Sam 'losing her baby'.
If he had stayed out of it, as Anna had warned, then she (Sam) most likely would have been home with Jason and not at the Rendezvous Motel. There is a likelihood that she wouldn't have gone into premature labor because she would not have had extra stress, but if she had Jason would have been more easily able to take her to the hospital or at least get her and the baby there. Plus, if they didn't make it the penthouse is a nice place to give birth.
If it was me, and I was tangled up with a married, pregnant woman, I imagine I'd be overcome with guilt and hightail it back to my own wife and kid. (and not be overly eager to call the husband out on 'sending me a message', no matter how arcane the delivery, or ill timed.). I would probably feel too guilty and responsible to press charges, and feel like I deserved the beat down on many levels.
Of course, Jason is now plagued with guilt because if he'd only accepted the baby sooner Sam would have been safe at home and never have gotten so deeply involved with McBain, nor left. He also has to feel intense remorse for keeping McBain from taking Sam to the hospital.
Sam's guilt will come out in huge, crushing waves.
That she put her baby in danger by being at the Rendezvous Motel instead of at her mom's, or home, or anywhere else. That she left and didn't fight harder to make it work with Jason, to make him love and protect her baby. That she didn't KNOW something would happen.
Well, This is what I would write before the switch is inevitably discovered.
Guilt can make for great character movement and growth. Sam can become stronger, more independent, less reliable on Jason to define her as a person and more like the 'old Sam' we once knew.
Jason could become more compassionate, forgiving and loving, much like he was in the old days with Robin and in brief moments alone with Sam here and there.
McBain could go back to his family. He needs to remember them, go to them; leave. Jesh, if he was my husband I'd be there looking for him by now. Hello, Natalie!