She's not morally gray at all. It's been showed countless times that she's not. Dewpite her grief she understood it wasn’t ok to kill, and she didn’t even wish for the Eitou guy to suffer this long. She also never used others for her personal goals, she only used herself. For instance her childhood friend is truly useful but she respected her and cried when she found out she had no idea about her friend's trauma.
It's obvious that Yotsuha's family have secrets, especially her father. That Rei guy was somehow related to her family too (he knew her mom). The real mastermind is probably Yotsuha's father or someone related to her family in a way or another.
And she's not even a master schemer. She just did countless rewinds with many failures.
ok theory time... lowk what if its yotsuha from a different timeline? like a happy one where MC grew up happy and stuff and he like. accidently triggered someone yotsuha cared about to die and she decided to make it her life mission to make MC as miserable as possible? like yotsuha seems to be very capable of that, shes a master schemer and morally gray not to mention very presistent, how many times has she resetted the time to save MC? pluss the whole clover thing.... so yeah i think its evil diff timeline yotsuha