Yes the act was a little extreme, but in the end it was justified. The Jedi attempted an illegal coup against the legal head of state of the Republic just because of his religion. To make that even worse Windu was going to kill the guy without a trial just because "he's to dangerous" and mainly because of his religion.
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When the guy is shooting lightning at you, because you refuse to let him tear down democracy, I think it's safe to say he's too dangerous to let live.