Reb E – the minim weren’t agnostic. They believed in a creator, but made other serious errors, and were hostile to the Torah jews. They caused such damage that chazal made a bracha for them in birchas haminim.
The entire gemara is “nisht tzu farshtain” – Hashem created tumah; he isn’t affected by it, nor is he affected by anything else, because He is kulo pashut, as the rambam says.