There were proofs against Myrtle. Now we know that Fiona set up the acid-on-hand thing, and probably the psychopathic wall of Cordelia's pictures (or maybe it was real but not made by Myrtle), but all of this looked very bad when Fiona presented it in front of the council. I understand why they voted to condemn her.
That being said, about Misty. I think she has a very strong intuition. She could feel Zoe's magic when they were trying to resurrect Kyle, she could feel the bad vides in the Academy (and she was right; the Axeman's spirit was there, Fiona's evil, and Delphine LaLaurie was there too), she knew how to find Myrtle. Even the aligators were being wrongfully killed and she was there to revive and avenge them. Perhaps you're right, she's probably able to sense when an injustice has been made, an injustice that she can fix with her power: she brought back the aligators, brought back Myrtle, healed Kyle, and who knows maybe Zoe wouldn't have been able to revive Kyle if she hadn't been standing close to the morgue?
Speaking of Misty's power, am I the ONLY one here who thinks she is probably able to teleport? I mean think about it:
1) In Boy Parts she was "meditating in the woods" and then she felt Zoe's magic and it dragged her. The morgue's in town, how did she get there so fast if she was medidating in the woods when Zoe and Madison were doing the ritual?
2) Again in Boy Parts, she appears in the car out of fucking nowhere. Not only is it a car that she couldn't possibly know Zoe was going to use (Zoe stole it from the cop), are we also supposed to believe that Zoe somehow sat Kyle in the car and sat behind the wheel without noticing that Misty was in there??? They'd been driving for a while when Misty popped up and said "I forgive you :D", are we SERIOUSLY supposed to believe that all that time she was there and Zoe didn't see her???
3) Myrtle was burned in the middle of freaking nowhere in what seems to be a desertic area. Pretty damn far from Misty's swamp and forest. How the hell was she there? Why was she there?
4) In the very last episode, when Cordelia is playing piano, she's commenting that Misty should be feeling her feet getting warmer (from Fiona's powers getting poured into her body), Misty touches her feet, then Myrtle says "I'm told it begins with a tickle in the crotch" (or something along that), and Fiona comes in casually, saying "Actually, it begins with a migraine", then she asks about Misty, they turn around and... Misty isn't there anymore. She was in the room 2 seconds ago, how did she leave so quickly, and how did Fiona not meet her on her way out? Immediately after Misty was shown in Luke's house when he was taken outside, again, how did she get there so fast?
Either Misty can teleport, or there's a mix of serious deus ex machina and bad camera/time managing on the show. Since AHS has accustumed us with good standards and it's a season about witches, I'm going to go with teleportation.
Hell for all we know, we haven't seen it but she showed up after Hank abandoned Kaylee's corpse somewhere and she brought her back as well, I wouldn't even be surprised, Misty is always around to make things right when someone is wrongfully killed.