Can I be brazen and weigh in with a feminine perspective?
Your sister-in-law might be a complete shit stirrer, but from an outsiders standpoint.. your wife & SIL just CLEANED A SHED. Your shed, yes, but still.. let's simplify it for what it is, a cleaned shed. It shouldn't be the end of the world, it shouldn't merit a "knock down drag out fight". And I say this as someone who really loathes when people touch or move my possessions.
The real issue here is that you feel like your personal space has been invaded or disrespected, and that you feel like your SIL oversteps her boundaries in your home and in your life.
You simply have to try to cordially, clearly indicate this to both her & your wife. "I really appreciate the effort and intention behind cleaning the shed, but when it's messy, that's my mess to deal with, nobody else's. I'd feel more comfortable with you in my home if you can please manage to respect my personal space. Please understand that I respect your privacy and wish to be shown the same respect."
It sounds like your wifes intentions were pure, even if her sisters weren't. So I get that you don't want to take it out on her, you shouldn't.. but I wouldn't be afraid to tell her she needs to remind her sister to respect boundaries. After all, if one of my siblings was upsetting my partner, I'd take it upon myself to intervene, because them fighting amongst themselves is arguably way worse. Even if your wife is the most passive, sweet person in the world, she needs to be able to clearly define boundaries for herself, for you & for your household. If the SIL can't respect you and your wifes wishes, you have to pick between icing her out and sucking it up. Cause it sounds like neither of you are going anywhere. As it was pointed out by others, she may very well be projecting her own failed relationships/ unhappiness onto your happy marriage.. and it may not be deliberate but it's problematic either way.
And uh, thanks for reminding me why I'm happy that my partner & I's families don't live in the same state lmao