As far as why Mace assumed the entire order was at risk, it came down to basic understanding. Palpatine was the Supreme Chancellor as well as THE SITH LORD they were searching for. He was in control of not just the Republic,but also the Separatist and in turn realizing this Mace clearly understood the threat. Plus I think they suspected him for awhile according to other SW media,so having it confirmed just meant that whatever they felt the worse case scenario could be was now in effect

First off I highly doubt a Master of Windu's caliber would ever be affected mentally by the dark side. Secondly Windu beat Sidious with all his dark powers, so this is irrelevant