I am trying out RCS in my 2.5G DP tank and so far I have had no issues...it's been about 2 weeks and the 5 I started out with are all whole and happy, as far as I can tell. I think it depends more on the puffers. I also have ghost shrimp in the tank, and the puffers pick at their antennae but leave the rest of them alone. It's possible my 2 puffers are just mild-mannered, but there's no reason not to at least try it. I make sure to feed my puffers every day, which I think helps a lot, a quick little shrimp is going to look much more like dinner to a hungry puffer than one with a belly full of bloodworms. Also, my RCS aren't even fully grown yet, they were just the biggest ones at my LFS, they are all under 3/4".
I wouldn't hold out too much hope for babies though, unless you provide lots and lots of plant cover for them. As mild as my puffers are, live brine shrimp are their favorite treat, and I have a feeling baby RCS look a lot like brine shrimp to a hungry puffer.
If I were you, I would add a bunch of plant cover, especially dense stuff like java moss, and put in a few RCS as a trial and see how they do. If they disappear, you know, and if they don't then maybe you don't have to get rid of your puffers after all
