N.C.
First thing is first.....have you confronted the other woman?? Is there a phone number at the bottom of the email (maybe a signature from her work with address and number??)? If so, I would call her. If not, I would email her and ask her details. Come straight out and see if its his baby. She obviously knows he has a significant other, otherwise she wouldnt have to wait to call.
I think that maybe you would have been able to forgive that he had been with another woman once, but seeing that it is 7 months later and she is pregnant, why if it was a one night stand would she still be writting him and contacting him?? Where you able to read through all the emails? Did any of them hint to anything else? I would NOT stay with him. Once a cheater always a cheater and also, the fact that he didnt plan on telling you?????.....WTF. He obviously didnt ever plan on it. He was going to leave and continue to do his own thing while you wait patiently at home for him like the good wife that you are. And dont think for a second that there are not women where he is deployed. They are there and they are lonely as well so I am sure this will happen again while he is gone.
While he is away you should get your things in order. Whatever you need to do to get out of this situation. File for divorce, get your money situated, figure out how the things should be divided. This is a perfect opportunity for you. By the time he comes home your mind set will be in the correct state and you will have prepaired yourself for what has to come next. Your son is still young and this wont effect him as much now but if you wait and dont do it then later down the line this could come back to haunt you. He could do it again, or never stop or you could realize you cant forgive him. Then your son is older and realizes what is going on and that is just a harder decision.
It is going to be a difficult road but you need to do what is best for you and your son and it doesnt seem like your husband had either of you in mind when he was sleeping with another woman!
Be strong, Good Luck!