Emily, yes, it would be best for them to just feed them off or euthanize them and never use any of them for breeding again.

Megacolon usually pops up in wedge-blazed husky marked rats(high white), mostly blue colors like American blue and the lighter blues. It's weird that it happened in a split-capped black baby(yours), but that's how the genes roll sometimes. A friend of mine had a very late-onset male rat that didn't show signs for quite awhile, except that he was smaller and wouldn't grow.

If any of the 2 week old babies start showing signs of MC, euthanize tham and don't use them for feeding. They would start showing signs after they are starting to eat solid food, but are still nursing(early onset and deadly) . They can also start showing signs after they are weaned and a few weeks after(late onset and shortened life span if different diet is used).

I'm sorry you're having to get rid of so many rats, but since every professional (pet) rat breeder is trying to keep that out of their lines, it's very important to never breed any rat that could be a carrier.