The reason is that at his core, MC has a desire to protect in general, and not just Eliza. He doesn't need a self-interested reason to want to help them (though obviously he has one in addition here since he considers them friends or lovers). That's one reason why he helps Luna, Amelia, the pirates, and likely dozens more unnamed others as part of his work with the adventurer's guild.
It's obvious there's a disconnect between MC's core values and priorities and what you think they should be. But ultimately, this is a visual novel and not a freeform role playing game. We may be able to influence some things with choices and Light/Dark path, but certain things are going to be immutable.
Revenge and protecting Eliza are important things to MC. But so is adventuring and protecting all his friends/lovers and people in general. I don't foresee that changing any time soon.