Yep, the tool you're looking for is called a compiler. :)
Seriously, if the programs submitted are exactly the same except for the identifier names, compiling then (without debugging info) should result in exactly the same output.
If you do this with debugging turned on, the compiler may leave meta-data in the executable that is different for each executable, hence the comment about ensuring it is off. This is also why this wont work for Java programs - that kind of info is present whether in debug mode or not (for the purposes of dynamic introspection).
EDIT: I see from the comments added to the question that you're observing some submissions that are different in more than just identifier names. If the programs are still structurally equivalent, this should still work.
EDIT: Given that the use of moss is a requirement, this probably isn't the way to go. I does seem though that moss has some support for comparing assembly - perhaps compiling to assembler and submitting that to moss is an option (depending on what compiler you're using).