User blog comment:D. Cello/Assassinews 03/05 -- ACWiki's Fan Section and AC3 first trailer/@comment-3979092-20120307015423/@comment-1153722-20120308083131

Not many people in the Assassin Order find William to be a sympathetic and nice individual; look at Shaun's remarks to him in ACR. William does indeed not care much about the lives of the Assassins, as proven to tasks he gave to Lucy and Clay. The Templars do want peace in the world as much as the Assassins do, but their methods differ; it is not unlikely for Lucy to prefer the Templars over William.

Lucy could have easily been told by Warren to request a rescue team only in order for the team to be purposefully exterminated. Though since Lucy already got Desmond out by herself in AC2, I don't count that as a contradiction for The Lost Archive.

Lucy took Desmond to the Assassin hideout first, until Warren came to pick up the Animus tapes from there; that's why he ambushed the hideout, to not draw suspicion from Desmond, Shaun and Rebecca about Lucy's Templar ties. He allowed them to escape to another place where Desmond would feel comfortable.

I'm not saying I support everything Ubisoft does, but this is just to point out that it's not necessarily contradicting to anything, and to me this way the story is more interesting than Lucy just being the protagonist's mere love interest and eventually getting a happy-ever-after.