I don't want to hear from anyone about how ZUN is biased towards Aya when we're on what feels like our 50th "Marisa seeks something out for her own gain, discusses it with Reimu, and it backfires in the next chapter" arc.
Yuugi is known for hating cowards and liars, and valuing strength. She'd appreciate that Mizuchi wanted to become a youkai rather than take the coward's way out and die, and would very much take issue with the perceived hypocrisy of Hakurei Shrine.
Oh look, an actual who dunnit.
Could it be Yukari? We learned she's the one speaking to Reimu, and this kind of plot is usually her doing.
Could it be Suika? She's friends with both Reimu and Yuugi and isn't opposed to some trolling.
Could it be Ibaraki Douji? With Kasen helping Reimu, and...
Miko sure will regret this once she thinks she has all the youkai rounded up, only for a certain newspaper to release compromising pictures of her and Byakuren together.
Former Hell =/= Beast Realm or the various other Hells for that matter
Also I think you're severely overestimating the amount of time Former Hell stays quarantined, Reimu is on her way to deal with Mizuchi once and for all, give her a few hours and it'll be open again.
Yukari has a recorded history of abusing Ran, and very few were made aware of this plan that had them be trapped inside this limited area with an escaped convict capable of putting them in a coma for days on end.
In Forbidden Scrollery and Lotus Eaters, Aya, alongside Mamizou are responsible...
*A Kyouko with the combined magical energy of Yukari, Yuyuko, and multiple gods. Don't forget that when Mizuchi was controlling Sanae, she instantly teleported behind Marisa and knocked her out with a single attack lol