Pressing mudras too fast is a problem for exactly the reasons described. Given what I understand to be technical constraints, I think that the actual solution is to grey out mudras that have already been used.

That being said, I actually do think that the mudra system is a good, simple way of capturing the ninjutsu vibe (ala Naruto). For it's flaws, I enjoy it! (There was that one Naruto game back in the day that had you do hand seals using joystick combos - it was a lot of fun but way too twitchy for this style of MMO. The current mudra system is a good balance.)