Well there are two ways already. VisualHub has been updated to 1.31 which is able to include AC3 5.1 audio into the AppleTV files that it creates. I would assume this is mainly used for people who are downloading illegal MKV's off the internet and converting them for viewing on their AppleTV.

If you have a DVD collection that you've been waiting to convert for your AppleTV, and preserve the 5.1 audio, HandBrake now has some beta releases that can do just that!
WARNING: This is a beta build from the HandBrake SVN, and should be used for testing only - not production use.

Select your ISO or DVD source, then on the "Audio & SubTitles" tab, select Codecs: AVC/H.264 Video / AC3 Audio.

By the way, I highly recommend that you use Constant Quality with a setting of 66 instead of specifying a bitrate and either single or double pass settings.

NOTE: you will need to change the extension to M4V in order to play the files (or just save them to M4V in Handbrake instead of the MP4 default.)

You can download the beta build of HandBrake here.

MetaX seems to be tagging these files just fine, the cover art and other text info shows up for me great!