Well it is true that normally MotS "requires" JK to run. This takes the form of (again, iirc) that once you install MotS, it asks for a one time check of the second JK1 CD. So that might be hanging it up. Otherwise though you shouldn't need JK to play it at all. If that fails, you might just be able to put the JK_.cd file (from the second disc) on a Cd and check that in.
I'm pretty sure Dark Forces 1 is the only game in the series that REQUIRES you to install the game in a specific folder (C:\DARK).