I had to look up ATV to answer your question. I hope you're referring to the Automated Transfer Vehicle, a bigger resupply vehicle being built by the ESA to service the ISS.

I looked at the physical size of the ATV and it appears that it would fit into the Shuttle's cargo bay. There are a few serious issues that would need to be addressed.

1. Solar Arrays: You'd need some way to Fold or get rid of the solar arrays. Perhaps they could be left at the ISS and attached for more electrical power, otherwise you'd need to find a way to fold them up or throw them away.

2. Propellant safety: Esuring any residual propellant from the propulsion system is safe to transport. Leaks of hypergolic propellants or inadvertant thruster firing in the cargo bay would be most unpleasant.

3. Shuttle Center of Gravity (CG) limits: Loading the Shuttle is a fairly tricky process. I've read that the CG range for the Shuttle is only about a foot from the most forward to the most rearward limits due to the nature of its double-delta design. Like virtually all aircraft, too far forward a CG and you'll have a hard time raising the nose for landing. If the CG is too far rearward, the Shuttle becomes unstable and difficult to control. Since the ATV is designed to carry up to 5.5. tons of waste from the ISS (intended to be burnt up on reentry), it'd be very important to make sure the CG limits aren't violated.

4. Shuttle weight limits: I've read that the cargo weight limit for a returned payload is somewhere around 20,000 pounds. It sounds like a loaded ATV might be heavier than this.

5. You'd need to carry proper mounting hardware to secure the ATV in the cargo bay. Making sure the ATV mounting hardware doesn't interfere with the hardware needed to carry any payload being delivered by the Shuttle. It'd be great if the same mounts could serve both purposes, but it seldom seems to work out that way.

If the safety issues can be resolved, and there's probably no good reason they can't, then I don't see any show-stoppers with the idea. Whether it'd be cost effective is another issue. I'd hate to be the poor guy who has to dispose of the waste (probably mostly feces and other similarly unpleasant stuff).