Everything in the prequel trilogy is manipulated by the Sith...and you left mention of their involvement out completely.
It's irrelevant. A decision can only be justified by the decision-maker's knowledge at the time of the decision. Not a single prominent figure even suspected Palpatine was behind the CIS, at least until Anakin tells Windu that Palpy is a Sith. Even then, they don't have any actual evidence that Palps is behind the CIS, except for the legendary Rule of Two.
Unless there's a Republic law against Sithery, the Jedi had no grounds to arrest Palpatine - Mace certainly had no grounds to threaten to assassinate him. As a sworn Jedi, Anakin was bound by oath to protect the Republic, and Palps was the legitimately elected leader of the Republic. In a sense, Anakin would have been violating his oath if he didn't attack Mace.
As for the clone wars in general, well, wars are never really justified by anything other than power plays on both sides.