I've used MKVTools to quickly make mkv's into mp4's with "passthrough" for the video. Basically, (from what I understand) it changes the container without having to process the video.

It works with my Xbox 360 and PS3 but I'm having trouble with playing them on the Apple TV. iTunes will accept them but I get stuttering even when playing locally on the Apple TV.

Another alternative would be to use Quicktime Pro to export the mkv with the passthrough option selected. You would need to install Perian first in order for Quicktime to open the file.