Why not run a parser that removes all comments over all code that is turned in. It's easier to read the code with no comments and if there are no comments the sections that should be commented really pop out (you can then check to see if there are indeed comments in the original file).

Simplistic comments actually help a lot when learning (even if they are just a reinforcement). Quite often our students write the comments first and then fill in the code which is perfectly fine.

It's also more interesting to let them freeflow it and then explain later why it might not be a good idea. The learning effect is stronger if they can go back and read their own overcommented code.