Always felt the whole romanced Jacob situation in ME3 was completely out of character and bad writing, myself, precisely because he does seem to believe strongly in personal integrity in ME2. His disgust with his father's actions showed that.
Then I seem to be in the minority here cus I quite liked Jacob on a personality level.
So he clashed with Thane a bit when Thane joined up. So, what? Its not like it led to continual animosity. Jacob was saying he didn't trust people who kill others for a paycheck. Turned out that wasn't quite what Thane was about, ultimately, but he didn't know that at the time. This was their first encounter. Heck, even Garrus admits to reservations about the guy in the Citadel DLC. They were legitimate concerns at the time, imo. And Thane was problematic all on his own with his initial insistence that he had no moral responsibility for the assassinations he carried out. Ultimately, everyone got got over it, though.