Hi MrsMxy!
I figured few, if any, would have the frame of reference for the game. I'm glad I was able to make it at least understandable for you. They could have gotten his memories in a number of ways (in the games - or at least the two I've played - it's been linked to an item that was important to the assassin - in Odyssey, for example, it's the broken spear of Leonidas that acts in place of the traditional hidden blade on the arm gauntlet). Maybe Abstergo got permission to borrow the journals, maybe Clark the first had a lucky penny he always kept on him, etc. I would also lean toward the memories being linked to the bloodline - the fact that it's Clark the Fourth and not some random guy.
You're right that the relationship between Lois and Clark would always be unbalanced. She can only do so much to heal him (and he to heal her, making amends for what he did). It's Lois and Clark, so I don't doubt that it would have worked out in some fashion or another, but it would NOT have been an easy road, not by a long shot. Even with a lifetime of therapy, Clark would still be stunted in so many ways from his upbringing. He would have had a very hard time indeed functioning in normal society after that - even with Lois by his side.