It sounds to me like you think it's much worse than it really is - it sounds very much like my situation growing up. If she isn't dedicated to forcing them into church every Sunday there shouldn't be a problem. Just make sure she understands that you want the kid(s) to make their own decision, and not have either side forced on them. The bigger problem (if any) sounds like it'll come from her family (or where you live if it's somewhere like the bible belt, which I'm guessing it's not).

As for the specifics you mentioned:

Let her get them Baptized if she really wants; It'll make her and her family happy and the kid(s) won't remember it anyway. Also, by forbidding it you're technically admitting that dunking the kid in water actually holds significance. There is no "atheistic creed" demanding un-baptizing.

Let them celebrate Christmas and Easter; All kids really care about is that it's fun... and candy... and presents. Also it gives them something to look forward to each year. On the more cynical side, when they learn of the GREAT SANTA/BUNNY CONSPIRACY it may help plant the seed of doubt in their belief of ridiculous things. For the most part, just make sure they enjoy it and have fun (and get the biggest and bestest presents on the block, thus solidifying yourself as the awesomest dad).

If she wants to be married in a church... well, whatever. As far as I'm concerned, formal weddings are really just a chance/excuse for her to dress up like a princess and be the center of attention for a day (and spend all of everyone's money). It's her only chance to do this and she's probably been looking forward to it her whole life, so let her have her fun. Again, the ceremony doesn't really mean anything, and being in a church isn't going to immediately convert you. If it's a matter of "pride"... well, if you really love her, then can it. If you meant she wants to force the kids to marry in a church, well, that's the kids' decision not hers.

Just to give you some background on where I'm coming from with this: My mom is a Christian and had me baptized and raised Christian. I went to church every Sunday until first grade or so (my pre-school was actually in the church) and I participated in the weekend youth activities. I believed in God as one would believe in Santa until sometime during middle school when it just kind of hit me that I wasn't really "Christian", and that I didn't really believe in a god. A while later the subject of religions popped up, and I started asking my dad what I thought were really controversial questions about Christianity and religion in general in hopes of turning him away from religion; I was unsuccessful because oops, he's an atheist.

For the most part though, let them figure it out, but prod them in the right direction. Try to get them interested in different sciences at an early age. If they're interested in history help them understand that; A big part of my switch probably came from simply enjoying stories and learning a lot about Greek, Roman, Norse, Egyptian and Indian (American) mythologies. Let them watch Cosmos if it's playing while they're growing up :P (if it keeps their attention), but try to keep them away from too much regular programming. Answer all of their questions, and if you don't know the answer help them look it up (and if you DO know the answer, and you know a cool/fun experiment to show it, pretend you don't know and have them do the experiment).

Can't think of anything else right now, but tl;dr: let them do her fun or boring Catholicy things, and while not forcing atheism on them, pique their interests in science, history, science, literature, science and/or the arts (and science). And heck, don't even tell them you're atheist (for added troll-dad points when they "break the news" to you later in life).