Yes it could well be fine, you could pop a bit of iodine on that navel area now to stop any bacteria. I would think totally the same about the others pecking at it and making it worse. As its been a straggler from the hatch it's going to be weaker than the others and I know with chicks the stronger ones always make a bee line for the weaker ones of the group. Being in the incubator will give it time to rest in peace and quiet from the others.
it will be ok.
