D.L.
Honestly, I think religion is one of your last worries with Robert. First of all if either of you were devout Christians (Mormons are Christian) then you probably wouldn't have had a child out of wedlock. That's not a judgement, just a statement that neither of those religions support premarital sex. So, unless you both found religion since then, religion might not be a big issue in your relationship.
What I would be worrying about more is what kind of father and man he is. You said that he now accepts being a father. What does that mean? Is he active in Benjamin's life? Does he provide child support? Is he a good role model for your son? Why did it take him 2 years to own up to being a dad? What kind of a dad will he be if you were to have more children? Is he now in Benjamin's life because it's convenient now that his marriage is failing or because he truly is stepping up to be a real father? These are a few of the many important fathering questions you should be asking yourself.
As for what kind of man he is... Why did he marry someone else the same time you were having HIS son? Why is he coming back to you now? Is he lonely? Is he the kind of man that always "needs" a woman in his life? Is this a pattern he will most-likely repeat - jumping from woman to woman? He sounds like he falls in love quickly without getting to know people or possibly has affairs.
None of the answers are my business - just things you need to seriously think about. It sounds like you had a whirl-wind relationship and that you don't really KNOW each other. Personally, with the track record you briefly mentioned, he is not one to stick around for, but that's your decision to make. The MAIN thing to remember now is that you need to take things slow and don't introduce him into your son's life as a boyfriend until you are positive that you want to go down that road. There is NO reason that Robert cannot be a wonderful dad to Benjamin and not be in your life romantically - which is really where you guys should start. IF down the road you are committed to making a relationship work (couples counseling at either one of your churches would be great) - THEN you could move in that direction. Don't confuse your little boy and get his hopes up for a man that might not stick around.
Oh, and to answer your question about religion... if it is that big of deal for either of you, would the other be willing to convert? If not, then you choice is to either support each other in each other's religion OR not start up a relationship that cannot work. Please, please think of some of the bigger issues I brought up. I wish all the best for you and your little boy!! :-D