Is there any way to stream non-MP4 content through JRemote?
Not yet (well, not video, which is I assume what you meant).
It is on The To Do, from both JRiver and LesPaul. I don't think the changes needed are extreme, though. Transcoding/streaming works on Gizmo (Android) for many devices. But I think JRiver needs to do some work to make their transcoding/streaming system work with the right settings for Apple devices.
From the last look I had at it: They were close. They're transcoding to H264s in a TS container, and serving via HTTP, which is all right, but it still doesn't work. I think either the H.264 "profile" they're using isn't quite "iDevice-compliant" (though the iPhone 5 is pretty forgiving and I tested with that), OR the pseudo-streaming they're doing might be more simplistic than the Apple device is expecting, which causes the proper "streaming handling things" to not happen, when they could if the same content is wrapped and served differently.
Almost all of this is stuff JRiver needs to do on their side.
For now, the best is to use JRemote for music, and something like AirVideo for video support. That's not ideal as you can't see and browse by your tags and views in MC, but it works for now.
When we discussed it last as I tested, JRiver said that (after the Mac version comes out) some of their big "streaming priorities" are essentially this: making video playback work remotely via MCWS no matter the client (within reason).