In my opinion, the show is forcing the viewers to see forced drama where there is none. You are right, based primarily on that logic, Winn should also be held guilty, because one of these days he may fall off the hook and be just like his father - The Toyman. However, DEO had reason to suspect that Lena was working with her mother all along due to the fake footage that they saw. And only Super Girl was willing to believe that Lena is innocent, because the plot requires her to be friends with Lena no matter what (kind off like in Smallville Clark only seen the best in Lex, and only after Lex started to show interest in Lana did Clark gradually became to be distant from him (not because of his constant snooping around)) and others to mistrust Lena no matter what. It's just the way this show is made out to be. :)

The Luthors in general have a very dark history. Plus Toyman basically snapped and went crazy. A lot of people trusted Lex. It's unfair to judge Lena because of her family but I can understand why people would.