Since actually throwing them away isn't an option, refilling stamina is the dumbest thing I could possibly think of to do with flower gems. Not that I would do it, but even refilling raid points is a better use since there's usually some time when there are more important bosses than points.

It is a good idea to expand your inventory space to some extent, but when you get to the point where you're comfortable the rest should go toward gacha rolls, 6* or not.