I notice some of those retailers also have a good supply of the kit lenses selling separately.
I think they are breaking the kits to maximize their profit.....some of the kit lenses are dirt cheap at that level.
I see no harm done and often the bodies are at very good prices
No worries. I recently bought a body-only 40D that came from a kit box. The camera is new and the price was great. The only problem I can see is if there is an active mail-in rebate program (run by a financially solvent company), and the SKU was removed from the box by the vendor, then you couldn't send it in for the rebate. Of course, that's not the current situation.