Sure, sure, Elias is the first person to value Chise — the first person to call her family — but does she really have to say that she belongs to him? He then proceeds to lick her bleeding wound. Ugh. This is the problem with unconditional love. On the surface, it sounds amazing: “I’ll love you no matter what! I’ll do anything for you!” But is it actually healthy? Should you always love your spouse even if they cheat on you? No, of course not. Should you always love your parents even if they abuse you? No, of course not. Should you always love your child even if they grow up to be a terrible person? Well, you know what my answer is. We only assume unconditional love is beautiful, because that love goes relatively untested. Chise doesn’t care if Elias lies to her about the Sleigh Beggy business. This isn’t much of a test for her unconditional love. But things would get a whole lot more interesting if Elias was actually morally grey or perhaps even flat out evil. Would Chise still stick by him no matter what? That’s when you really put unconditional love to the test, but I don’t expect the story to ever go there.
Free to now cleanse the corruption, Chise enters Matthew and Mina’s memories. There, she learns that Matthew had been tricked by an evil sorcerer into murdering cats. The cats’ blood served as a necessary ingredient for a medicine that would heal Mina’s body. That was the theory, anyway. Unfortunately, she was not healed when Matthew poured the vile liquid down his wife’s throat. Oh no, that definitely didn’t happen. Instead, her entire body instantly melted into black sludge. Ooooh, so she’s part of the present-day corruption too. Anyway, it turned out the sorcerer was simply using the couple as a guinea pig, but instead of blaming the right person, Matthew somehow convinced himself that he didn’t get enough cats’ blood. He needed to have killed more cats, and he should go do that right now! I guess he thought he could still save his sludge of a wife. As soon as he stepped outside, however, Mina’s cat Tim revealed itself to be the king of cats, and killed Matthew with one bite to the neck.
Back in the real world, Mina apologizes to Chise for showing her such a painful memory. Nevertheless, the former would like the latter to erase her and her husband’s existence. This way, they can finally move on. The characters mention something about souls being part of a cycle. Are they implying reincarnation or something different? How does Mina know any of this, by the way? Do you gain knowledge by being a sludge for centuries? No matter. In the end, Chise refuses to erase those two. It sounds like it would’ve been painless for them, but the girl is nevertheless too sentimental about a couple she barely knows. Perhaps she is impressed by their unconditional love even though it drove the husband to murder innocent cats. As a result, she enlists Ariel’s help to allow the couple to pass on to the afterlife without being erased. So despite his crimes, Matthew gets to embrace his wife one last time. Does he really deserve it, though? I suppose it’s been centuries since he killed those cats, and it’s not like he could do it again. Part of justice is recidivism, after all. So you could argue that he’s done his time. You could also argue that he only did it out of love, so we can be a little more lenient. You won’t convince me, but I can still understand why some people would hold those positions. Unconditional love is powerful, but it’s also dangerous.
Moe Sucks 
I did told you that there are some “stuff” on the road to the conclusion that drag the entire thing down. The fans that I discuss about those stuff with told me that this is just the beginning and those stuff are obviously wrong, but the more I read the manga the more I’m certain that the author is serious about the entire “Chise X Elias” thing. Yeah, just like a lot of other stories about “wrong” relationship, this story is not about the characters realizing that their entire relationship is problematic and dealing with it. This story romanticizes the hell out of that stuff.
This is also why I think that the side characters are much more interesting because unlike the main characters, these side characters are not bound by some contracts to be good and pure for the lack of better words. Matthew and Mina is pretty much Elias and Chise, but something has gone wrong. And Elias and Chise are already in the wrong position to start in the first place. I agree with you that Elias isn’t going to go evil or even morally grey. And if he ever do something that skirts the morally grey area, I’m sure that he’ll be stopped by his friends and/or Chise before he does it, so he can be “morally grey” while still remaining as a pure character. He is not going to go down on the path of no return just like Matthew, and it makes the entire thing boring and predictable.
As for the conclusion, it’s just standard animu stuff. We all know that there is no way our good and pure heroine will erase those two, so the story goes to the standard feel good conclusion where everyone is happy happy.
It sounds you’d make a terrible parent. You’d better never have children.