I can think of one reason: To keep people on a server, who have a decent EU production, from hollowing out exceedingly large areas with almost no effort. While you can do that with a nuke, the parts of the MFFS are reusable indefinitely. Heck, if they could be moved with Frames, they would make an amazing boring head for a TBM. .... Consider that a suggestion! Still, I agree that there should be a cost associated with removing blocks. Perhaps not the exorbitant costs suggested, but at least some reasonable cost, by default, and a setting in the config file if you should want to modify the costs.
Perhaps there could be a forcefield (or upgrade) that'll remove blocks, store them, and replace them later? Some sort of 'Stasis' field? You would, of course, have to account for any blocks placed in the area, perhaps if there's a block in 'storage' and when you try to 'un-stasis' it on top of a block that's been placed in the same location while the field was on, there could be a 'Reaction' (feel free to use your imagination here)?
Though, considering the variety of ways in which the different mods 'place' their blocks, it very well may be more work than it's worth.