I had a similar issue for the purposes of archiving. I serve as videographer for a Govt. entity and needed a viable format for archiving our work that was non-corporate. Jpeg2000 stands out as an excellent choice for this.
I had previously been using Sony Vegas as it had a built-in J2K codec that used the .MOV container. While this worked, I felt it lacked quite a lot because it didn’t allow for any control or manipulation of how the codec was used. As I learned more about the power of the codec, I wanted something more fully featured.
Eventually, I purchased the Morgan Multimedia Jpeg2000 codec. It stored the files in an AVI container, but it game access to all the major controls available for the codec. And it was VERY inexpensive. It’s certainly not idea, and can be finicky, but it’s effective.
There are apparently other implementations of the codec out there (I believe Mainconcept has an encoder) but the problem becomes one of playback.
The benefit of the Quicktime implementation is that any Quicktime capable player can decode the stream and play it back. The AVI container is less standardized as I’ve found.
The primary drawback of the MXF container as you’ve noted is that there isn’t a lot out there that deals with it. The VLC player (by VideoLan) is what I currently use for my playback of MXF files, but the MXF standard is SO loose, I can’t guarantee what will work and what won’t. You might try this player and see if it works for you.
For archival purposes, I include a copy of the player, codec, and video files on each disk, so that should that stuff be needed down the road, all tools for opening and working with the files are contained on the same disk. I also keep a low-res proxy on that same archive disk so it’s possible to view what’s there in an easy manner.