But it changed a whole lot of files. Did it change anything essential that would make my game unplayable in the future?
Most likely. TESTool is useful for creating a Merged Objects file, and maybe cleaning those mods that
specifically need cleaning, although I hear there's a few other tools that do a better job at that. Under no circumstances should the "Just Fix It!" or Merged Dialog options be used, due to an alarming propensity for breaking mods (and thus, when used in an existing game, turning your save into a fireball visible from Pluto).
If you have a backup of those .esp files that were changed, I would use those to overwrite the files TESTool messed with. Or just download the mods again and overwrite the .esps, if it comes to that. If you haven't saved your game with the TESTool'd esps in the mix, you should be good to carry on in your game as if none of this ever happened.
Meanwhile, if you're really looking for a magic wand to wave over your load order, http://code.google.com/p/mlox/wiki/Mlox is enormously helpful, especially when combined with Wrye Mash.