Especially now, since the addition of other Minecraft entries (separate save entries for worlds, textures, etc), there's really little to no need to save the whole of the folder. And of course, for the very few people that would be affected by the change (maybe some one-off mods that sit in an odd directory not covered by GSM), they can always make a manual entry, that's kind of what it's there for. But I think the change of removing Full from the default list will be more beneficial to more users, if they're experiencing the same lockup/slowdown I am.
EDIT: I think the size of the folder itself might be causing issues. In my particular case, running GSM caused it to lock up entirely when getting to the Minecraft (full) entry, for several tries, and this happens often. This particular time, I noticed my Minecraft folder was about 400MB (not terribly uncommon if you have a few mods and texture packs installed). After I deleted some duplicate files, I got it down to 300MB, and it was able to run correctly. However, like I said, I feel I'm likely not the only one having this problem, as this game is prone to a very large main folder size.
EDIT2: Nevermind, even after deleting 100MB of files, it still froze GSM when trying to scan the directory, it just made it farther before doing it this time.
And I can't just "ignore" the entry, because this is on a new install and I'm unable to get a full scan to finish (required for ignoring entries).