That was the essence of Proven Guilty. Molly had good intentions and yet ...
Actually, Molly's intent is not very pure. It is proven by the fact that Rosy's damage is far less severe compare to the damage done to her ex boyfriend.
As mere mortals, wizardkind has a hard time mastering their intent, their magic therefore is not as well controlled as pure supernatural being like the fae. The very nature of mortal free will does not allow for such a pure intent in a mortal. It is the very reason for the existence of the murphionic field.
Even though Rosy's damage is mitigated , I doubt Molly does not feel a least a bit of anger and jealousy against Rosy. The girl did take her boyfriend away. and when she decided to invade the minds of her friend and ex boyfriend, I doubt there is no slightest bit of dark excitement involve. The dark side of altering another's mind is a popular subject in pop culture, and unless Molly already achieve a mental state of an enlighten Buddha, saying that her intent is purely good is most likely a false assumption.
If you ask me, intent does matter, but in a case where magic is used to kill a mortal, or breaking any of the 7 laws for that matter, a case where there is pure good intent involve might as well be none. It is only a matter of degrees, and it will be reflected in the level of taint received and how it will impact the wizard's sanity and control.
Judging this kind of thing is rather difficult, so the white council just kill everyone they can.
There are alsow ways to avoid the taint, or at least that is what the council believes, which may or may not be true. Using an enchanted swords, Transforming into a wolf and biting a mortal's throat. Using kinetomancy to speed yourself up and stab someone with a knife with that speed advantage and so on.
Up until now, I am not even sure about whether or not Molly's tenure as the rag lady tainted her. The deterioration of her sanity might be an indicator of the taint, but due to exposure to the blood ritual in CY during book 12 + her involvement in Harry suicide, Molly's sanity is already taken a lot of hit. It is enough to explain her condition without blaming it on black magic taint. The council did want to execute her, but the council would do that even if Molly stay at home and be a good girl all the time. The fact that Harry is dead is enough for the council.
It muddies the water, And as far as I know there is no WoJ confirming this issue either.
My best guess is no. Molly's illusion, though ended up in mortal death, does not taint her more than when a warden use swords to cut down warlocks or supposed to be warlocks.