I understood why they did it due to the canon timeline. HOWEVER, it also contradicts the option as well as many point out. In a way, I also understood the complaint as well.

Even more so to further my contradiction remark is that after the identity of the cult revealed, your option are to kill or spare.

Killing that person would have ended the creation of The Templars, and without them there wouldn't be the creation of the Brotherhood; sparing that person would mark the origin of The Templars in Odyssey, whereas Origins mark the origin of TY he Brotherhood. Yet they gave us the option anyway, whereas the DLC didn't. Damn the paradox it seems.

What is also known is that who is to say that either Alexis or Kassandra are the main? The male or female? The answer as players are Yes. Jest, but it's true. The fate still winds up the same for either of them, but the choice is our own, and given them the path the player gives them.

Also, the beginning of the game made clear on choices especially on whether to spare the family but affects the island of a plague; or have the soldiers kill them in order to save the island?

So, why not give a second option for the DLC? This does indeed forced the players in one path.