I've been working on this for days, and I couldn't do it on a mac.
I found some good leads for windows, but instead of installing bootcamp (which requires a defrag) and going through all the trouble, I just bought visualhub for 23 bucks.
Here's some tips for people still trying to do it without conversion:
http://forum.videohelp.com/topic349617.html
MKVTools for Mac
Videora for PC.
h264info for pc.
You should be able to figure it out.
There's a very easy to use windows tool
H264info will let you change the properties of the H.264 video file, after demuxing using MKVTools or something similar. You can change to profile 4.1 very very easily using this h264info.
Good Luck.
for me though, I just used Visual Hub last night, and I'm very impressed.
I had Transformers 720P (566x1280 or so) H.264 and AC3 5.1 in an MKV that I got online (Septic version).
I used Visual Hub with AppleTV 5.1 Preset, H.264 encoding, 2 Pass, and Audio passthrough.
I haven't watched it yet but I skipped to an hour and a half into the movie and the video/audio is perfectly in sync, also I can't tell the difference between this and the mkv at all maximized on my 24'' monitor.
After work today I'll compare the two on my 73'' 1080P and let you know how it is.
I have compared the DVD Transformers with 1080P upscaling to the 720P .mov that VisualHub spit out (after 10 hours...), and the difference is amazing on the 73''.
I would go with visualhub for the time being because of it's convenience, ease of use, and guaranteed compatibility with

TV