|My guess would be that the black stains are from something in his poop while he was ill, possibility something with the pedialyte (no reason other than that's the odd ball in his diet). I very much doubt that two days in a pail would cause problems (I regularly went three or four). If he doesn't seem to be getting over the bug and you think the diapers may be recontaminating him, then I'd take action with bleach, but otherwise I think I'd try other things first (or honestly, I'd probably just do nothing and wait for the stains to go away).
A couple things that might help and won't hurt are vinegar and tea tree oil. Both have anti-bacterial properties. Vinegar can also help if you are concerned about build-up (although that is not going to cause black stains, so not the culprit here). You can wash them on hot with lots of vinegar, or you could pour straight vinegar on the stains. You could also use a significant quantity of TTO in a hot load or soak (have read 20 drops for disinfecting; not sure why that number, maybe because it's normal to use a few drops in a load and that's 10x normal use? not sure).
Those two aren't going to make the stains go away, but they could help ease concerns about thing growing in your diapers without using stronger stuff like bleach (or peroxide, which ME doesn't recommend, either).
I don't know that baking soda would help to disinfect anything, although I do use a baking soda solution as a fungicide/repressor for my plants, so maybe it has powers in this realm that I don't know about . . . It, too, isn't going to cause harm to your diapers.