It was possible that Stephen didn't fit into the normal Avengers moral code -- to be fair, he wasn't an Avenger and he had his own missions and goals and, from what Loki could tell, was willing to do whatever needed to be done in order to achieve them.
It was also possible that labels didn't generally work as cleanly as most would like. Loki wasn't a villain, and even when she had been considered one (more often than now), she hadn't really thought of herself as such. Admittedly there had been a lot of spite involved at the time regardless but -- well. No one was perfect.
"Maybe one can be morally grey and still a good person," Loki said after a moment. "Maybe there's no fun in the idea of ruling a hotel full of Avengers." She twitched a smile. "Or maybe the sex is just good enough to not care. We work, and he wouldn't dream of thinking to police who I'm talking with."