Marx saying "killing people and destroying property solves nothing" still makes me mad. Not just because Marx would never say a thing like that, but also game is a fucking killing spree simulator. Whole game you go into factories to liberate workers, kill templars and destroy their stuff. Why pacify Marx in a game where you kill people with your stabby-stabby mechanism?
I'd say it's a classic example of ludonarrative dissonance, I think. Violence is traditionally very conducive to quality gameplay.
The game's narrative in its core is created by, as someone else has pointed out, French liberals, so it's not surprising at all that it sends a message that's beneficial to the class of those who created it. They're not going to betray their own class by outright saying it's okay to kill the capitalist opressor. Maybe you should, you know, talk it out or something. Reach a bloodless agreement.
However, the whole Assassins' Creed series centers its gameplay loop around, well, being an Assassin, which means the way you make progress is, obviously, by killing people. So at the same time that it pushes you, as a game, to kill the templars and liberate workers, it also tries to pacify you, as a bourgie-friendly narrative. Otherwise it wouldn't be a very fun game. I mean... AC Syndicate is not exactly fun but you get the idea.