The bat files just change the directory and run the appropriate class with the correct classpath. You can just copy the bat files to local dirs and edit them to change the directory to where nand2netris is unpacked.
Alternatively, you can just distribute the package, which contains the applications and the project directories, so the students would run the tools from their own machines.
I've put the tools in a project on github
and added various improvements there. I tried to package the tools in executable jars, but there are still some resources, which they load directly from the disk. I'll try to fix that soon, but right now am a bit busy, so no promises...
I added an issue to the project, so you can just watch that if you prefer: https://github.com/itoshkov/nand2tetris-emu/issues/3