Yes, you can add a second 600EX, with one on-camera and the other as a slave, or get both off-camera by connecting one with an OC-E3 cord (or 3rd party copy).
You mention the high cost of the MT-24EX, but RRS gear isn't cheap, either. To get the pair of flashes out to the subject, you'd need another mount and a pair of extenders, plus a lens collar plate - close to $500 in RRS gear, plus the cost of the 600EX-RT.
I would probably not be inclined to buy an MT-24EX for use with just a 100L, but it's the right choice for an MP-E 65mm, and since I got the twin-flash for that, I also use it with the 100L. I considered getting the RRS setup above, a second mount plus a second extender (I had one already to get the Better Beamer further off-axis with the 600L) for the twin light, but I think that setup is limiting in terms of flexibility. Instead, I opted for a pair of Wimberley F-2 brackets.
So...my current 'ultimate' macro lighting rig is the MT-24EX in the hotshoe with the twin heads each on a Wimberley F-2 bracket to light the subject, and the 600EX-RT on the RRS bracket w/ extender as an optical slave to light the background.