I'd put this into the bug tracker, but seeing that all of the bugs are for the upcoming changes (which seems like a complete overhaul based on Direwolf's videos! I miss my pretty refined iron already! ), I'm pretty sure this would be obsolete.
I ran a test setup with a MassFabricator connected to an MFSU at maximum storage (in creative mode). When it produced 1 UU matter, I broke the MassFabricator. The energy used was about 170,000 - I'm accounting for the time it took me to see that it hit 100% and breaking the machine). The MassFabricator had no scrap in it, but that energy cost is the cost of having scrap constantly in the MassFab.
For now, I'll just chalk this up to the "teaser before the nerf". The nerf being that I don't think I can build up stacks upon stacks of UU-Matter. Granted, if I can put liquid UU-matter into cans...