I just don't think Louis would make a good killer, period.
To me, it would be more interesting to have him figuring out who Dexter really was (perhaps the marks on the hand are to show that Dexter & the ITK are brothers?) and wanting to be his sidekick, disciple, etc. Or perhaps use him in the role of trying to impress Dexter and Dexter having to make a decision on what to do about it (like, could he leave him alive knowing that he has all this proof of who Dexter really is)
Killing Harrison would be a bad idea and it would be repetitive. I mean, with everybody close to Dexter dying or disappearing, there's gotta be so much suspicion about him that it would be impossible to keep him undercover as the BHB.
His wife AND son murdered by 2 different big name serial killers? Come on now !!!