Jor-El was pretty villainous in the early seasons of Smallville.
According to Mark Waid, the big bad of Birthright was originally going to be a malfunctioning AI of Jor-El before Jeph Loeb, who was writing on Smallville at the time, told him that was what Smallville had planned. So, Waid changed his story, then Smallville dropped that plot thread and suddenly started pretending that the Jor-El AI hadn't been an asshat for a few seasons and claimed he was only "hard on Clark to prepare him for his destiny".
Damned shame. Birthright is great, but you can absolutely tell that Waid had rewritten that ending with the fake Kryptonians hired by Lex.