Well he sounds like a great guy and you are right, there are way more pros than cons. In my opinion, the kissing is no big deal. Honestly, if you drop a few hints he'll probably get better. Don't be mean about it, but be upfront. Think about it as if the wheels were turned, and he hated your kisses. Would you want to know so you can make it better for him?
Also, as far as religion, thats a person's own individual choice. I know it is extremely important to some people, but you should respect his differences. I know many couples who can work through that.
All in all, it depends on what you feel for the guy. If you are not happy and you just can't get past these two things, you need to talk about things. It's really nice of you to be so concerned over hurting him, but yuo have to do this for you.
Great guys come few and far between, so I hope you make the right choice.