I know Louisa doesn't owe Marcus anything because even though she has Jun's soul, she isn't Jun. What made Jun herself was her experiences and thoughts and the moment Jun was reborn, she was wiped a clean slate. It's like using the same computer but with different users, your account is yours and another person's is theirs. So if she wants to be with Graham, she has every right to do so.
I just wished that there was a chance for Marcus to be with the original Jun (unreborn)