Those issues are related to the icon cache; I don't think the cursors are. You picked up the mouse cursors by nuking ~/.icons/xcursor-transparent, and you won't put that back with gtk-update-icon-cache.

As for safety, it shouldn't be able to trash anything but your icon cache, and it shouldn't even trash that. Which is nice in theory. :/

Edit: Just saw your edit. I normally run fsck with -p and see if it errors; of course, if it does I still wind up doing the practical equivalent of -y, since I don't know ext2fs well enough to even contemplate a manual recovery. But strictly, no, -y is not safe.