I seem to recall them handling it poorly/unsatisfyingly, but maybe I'm being uncharitable given that they left in a winky reference to known MRA shitbag Jordan Peterson with no apology in which they literally refer to him as "Jordan the Wise". The reference went right over my head when I played The Messenger (which I loved), since I didn't really know who he was at the time, but I guess that's kind of the point. Sneaking being awful past the censors, so to speak. It certainly suggests a certain kind of attitude being prevalent/accepted at that studio.
Edit: Ninja'd!
I think my post that's being linked basically includes everything about how they handled it, so you can make your own judgements from that.
The one thing that sticks with me as an unresolved is the "without getting into how this line made it into the game, as the explanation would seem made up" part of the announcement they'd patch out the joke. It's good that they removed it, but I'm really confused about the kind of insinuation here that it was a big accident.
That being said, paying some attention to the studio heads since then, they both seem like basically mainstream liberals who are also maybe also kind of reddity dumbasses repeating memes like idiots without thinking it through, so my inclination is to believe that this was just thoughtless stupidity instead of malice, if you care about the difference. (I do, but I understand anyone who doesn't.)
For me, I never bought The Messenger despite it looking up my alley, and this upcoming game is a wait and see situation. If there's nothing like this in the next game, I'm personally willing to recognize their improved thoughtfulness, although I understand why anyone would be suspicious enough to write them off. (Especially when there are basically infinite games to play, books to read, movies to watch, etc. and limited time.)