Nothing in the game explicitly implies the things she does are because she feels guilty.
Dude. Once you reach the point where you're arguing there's no implication that Mio is motivated by guilt, you've wandered way off into the tall grass IMO. It's the second line of her character section in the booklet, and the third sentence of her character summary in the guidebook glossary. There are two entire endings where the dramatic moment is Mio catching Mayu before she can fall. The whole setup of the accident mirrors what happened with Yae and Sae, and it's why Yae's spirit is attracted to Mio just like Sae's is attracted to Mayu. Mayu knows that's the button to push when she wants Mio to stand guard indefinitely outside a locked cell instead of leaving for five minutes to get the key and Mio actually hesitates - that's not love and forgiveness for a sister she knows can't think clearly, that's a special kind of crazy that these two have been reinforcing between them for years. It's fundamental. Mio doesn't need to be doing a running monologue of her feelings for it to be explicitly implied.
Nothing says she isn't smart enough to realize that she did nothing wrong
It's not about how smart Mio is, it's about the break in understanding between Mio and Mayu that fuels the whole game. Mio knows Mayu fell on purpose, but she doesn't know why, and since they can't talk about it, she accepts the blame. She says, "If only I'd been there, holding your hand." She says, "I wish we'd both fallen together," and then, "This time, we fall together." I don't think it could be much clearer that she doesn't think Mayu's at fault for falling, she thinks she's at fault for not being there. She doesn't think Mayu needs forgiveness for doing it, she thinks she needs to atone for letting it happen. Her main concern is closing the rift between them, not making Mayu a better person, whatever that means.
Her actions in the game don't come across as being driven by guilt and self loathing but instead by love and forgiveness. I wouldn't have saw those qualities in them if there wasn't anything in the game or supplemental material to suggest that as being the case.
Well, I'm pretty curious to know what you think her actions would have looked like if they'd been driven by guilt. And I'd like to hear what specifically gave you the impression that forgiving Mayu is on Mio's radar, or that she thinks Mayu needs forgiveness. Just because Mayu's behaviour seems creepy and manipulative to us doesn't mean Mio has to see it that way.
I have to agree with Hex here, it really seems like you're ignoring and twisting a lot of stuff just to build a new idealised headcanon around one line from the guidebook, which doesn't say any of the things you're getting out of it. I get that you love their relationship and want it to be perfect, but you used to argue just as vehemently against the idea that Mayu had fallen on purpose or that she wanted to do the ritual. Now you've accepted that Mayu has issues, but it feels like you've just transferred that burden of perfection onto Mio. If Mayu can be messed up, irrational and selfish, then Mio has to be proportionately accepting, self-aware and pure of heart. (Not even getting into whether "Saint Mio spends the whole game forgiving her terrible sister" would actually be a positive thing...)
Like Hex says, I'd take Frozen Butterfly as a strong sign that although Mio might be vaguely aware of this stuff, she's been suppressing it rather than facing up to it, which kind of precludes any kind of acceptance. Mio learning to understand Mayu properly is a huge part of her arc and the main turning point of the endings - the worst ending is the one where she doesn't even try, and Frozen Butterfly is the second worst, because in that one she understands what Mayu wants and rejects it. Even though what Mayu wants is something dark. The story doesn't operate on a simple right/wrong axis, so acting like Mio's only options re: Mayu are forgiveness or anger doesn't work.
That was totally on-topic, there was a whole paragraph about Frozen Butterfly. How bout that symbolic headless doll?