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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I agree with you, but his time was overdue. And Windu & team didn't go their to kill him, they went their to arrest him. It was only after Sidious attacked them did Windu see the need to end it.