I don't see why Cowl can't be infected and be trying to do what he thinks is good at the same time. We saw that Auora was infected and she clearly thought she was doing good. Sure Cowl isn't as insane as her but we've seen that their are varying degrees of infection (cat sith was completely infected for example).
He might think he is doing the good thing if that makes him easier to manage by the outsiders but that does not matter for what he does. For what makes him act.
It is like mind magic. The smart thing is to change just enough so the subject will do what you want him to do. Outright possession is always less efficient and is only to be expected when other options fail.
But the motivations of the infected, the things that really make him move, are the motivations of the outsider managing the infection not the delusions used to keep him under control.
So watch cowls actions, not his words, to see what really makes him move.