In Scare Clark still believed Lex's spiel about the projects being Lionel's, for instance.

I've seen no evidence to suggest that the project in "Scare" wasn't one of Lionel's. And I remind you that, although Lex had been exposed to the virus later than the others, and thus had more time than the rest of them, he still chose to use an untested and potentially lethal vaccine on himself rather than using someone else as a lab rat. Not exactly 'evil' of him....