One workspace, two IDEs - Possible?
Are you willing / able to work with Xcode? There is a package called embedXcode that enables Arduino development on Macs – I'm just getting up to speed with it, but it does appear to allow you to work either in Xcode or with the Arduino IDE (the .ino file is present and is what you edit in Xcode). In my testing so far it appears that the easiest thing to do is to create a project using Xcode and then you can point the Arduino IDE at the project pretty easily, getting Xcode to pick up a sketch started in the Arduino IDE is currently beyond me.

From the point of view of your students I would think that you'd want to keep the .ino file rather than make them learn about the conventions of C or C++. It would also save you the hassle of somehow managing file names – although you could probably get make to do this for you.

I haven't looked into it at all, but I think you could do something similar with Atom (a quick Google found a blog post called Arduino Development in Atom Editor and an Atom package called nino that is described as a "Toolbelt for Arduino") or Emacs, or for that matter Vim is also like to have some Arduino support.