6/7/2014 Update
After some experimentation, I believe I was able to modify the NBA Audio Editor tool (which is open source) to be able to import tracks into 2K11/2K12 bin files. There were a few assumptions that I made about the audio format which resulted in one or two "hard-coded" changes I would have rather had a programmatic solution for, but so far in my testing all has gone well. A few facts about the format:
The header format is similar to the NBA files, but are shorter because MLB files have fewer packets per audio "chunk"
Each chunk is made up of no more than 5 packets
Each packet is 1,487 bytes in size
Each chunk has a filler at the end of it, the size of which is 8,192 - (56 + (4*PacketCount) - (1,487 * PacketCount)) bytes long
I believe the filler is primarily why the existing NBA tool did not work with these files, as it threw off some of the offsets the program was calculating (as well as other properties like file durations). Since this has been addressed, NBA files can no longer be used in this tool.
You should be able to feed the program any wav or MP3 file (whether it is the correct sample rate or not) and it should convert it into the correct format. From there, the program will filter the list of slots to only ones that are longer than the song you are trying to add. For best results, the duration of the new file you are replacing should be close to the original duration.
All that said, I want to release the preliminary version of the modified program so people can experiment with it. It is by no means finished, but it is hopefully a good first step.
While the program can successfully import files, exporting files still results in something unrecognizable, even though I made analogous changes to the exporting code. So unfortunately for now, I have disabled the ability to export .xma/.wav files. This means that there is really no way to preview which files you are replacing. I have stuck to editing jukeboxmusic.bin so far, and the order in the file is the same as it appears in the 2K Beats section of the game.
Anyway, a huge thanks goes to Leftos and nesa24 from the NLSC forums for their initial work on this - not being well versed in .NET C# programming, I would not have been able to build something like this from scratch. The program comes in a .zip file with a folder. Simply extract the folder and open the "MLBAudioEditor.exe" file and start changing music! As always, backup your original file first!
MLB Audio Editor v0.1.0.0