Will this system chain work?
Apple TV does not support USB audio, so no. You will have to use the toslink out from the Apple TV or consider toslink to USB conversion, if possible.
Will I be getting the quality I'm looking for going this route
You'll have to be the judge. I am very happy with quality of the itunes lossless/appletv as a source, YMMV. Your downstream components are very good, and many people consider itunes lossless/appletv/airport an excellent combination.
and can you think of a better method to go about this?
Consider using the Remote app on your iphone/itouch to control apple tv. I don't think you can control apple tv with your macbook. If you are just streaming music and not interested in the other apple tv functionality, consider using the airport express instead. If you are committed to ALAC, apple tv or airport express is the way to go, IMHO.
Good luck
