I also wasn't sure what you were asking - hooks or what hangs on them, but based on the responses from others, I'll continue along that vein.
I can see why you wouldn't want hard frames with sharp corners, let alone glass, above a crib. Yes, it will be ages before the baby can get up there, but you also have a 5 year old (I think) who may well decide to toss a ball or throw a truck... I know he's perfect (aren't they all???) but still...
I looked at Mykala's link and I think those hooks look great - assuming your older son won't cause anything to break even if the frame itself is still hanging.
But even if you take the pics down, don't spackle - I love the idea below of a quilt. My son's room had some fabric-covered shapes that looked like balloons, but you could do any sort of stuffed or fabric-based decor that just covers up the holes from the old hooks. It's light weight, and requires very little for hooks. Check resale shops if you can manage to get out. You can use 3M Command adhesive - easy to remove without wall damage - I use it for seasonal decor that has to be hung at a different height than the picture hook for the pic I remove temporarily.
I'd go for the least amount of effort!