Why not keep the IDE extremely lean (it already takes too long to download, and space is a big problem for computers at a school), but add a CLI that comes with it and does exactly the same things hitting the compile button does (not one of those sorta-kinda-works makefiles) so that after editing in whatever you want, you just setup a button that runs that program.
Really, it's much simpler to make than to explain. This way, you can use any program at all to edit your files, and if it includes a user-configurable compile script (which most sane ones should, but I really have no idea), you just put in "arduino -c file1 file2 file3.