Well, Jessica's 'betrayal' was big enough that it came to be known as 'The Jessica Crime' falling in love, and abandoning the Sisterhood because of it. The first example I recall hearing them use that term yields another example; Dortujla.
"Name: Dortujla. Sent to special perdition years ago for an unforgivable infraction. Memory said it had been a love affair of some kind."
"Odrade recalled gossip about Dortujla’s disgrace. “The Jessica crime!”"
I'm not sure there was anything else on the same scale as Jessica shown (hard to top, given that it produced a Kwizatz Haderach out of his proper sequence), but there is at least one more example of defiance that I can think of from the Prequels; Tessia.
Lady Tessia Vernius, wife to Rhombur was never indicated to have any direct instructions involving controlling or manipulating her husband, but she was portrayed as caring about him deeply and having his best intrests at heart. But her violation of their orders came when they demanded that she produce more children (not his) for the Sisterhood and she refused.
“My womb isn’t a tool for you to borrow whenever you like. I love Rhombur. He is my husband, and I will not be a brood mare for you.”
“It will not be an extraordinary commitment—three daughters, no more, with different fathers.”
“I have other obligations now. I am also a wife and mother, and I will not turn my back on all that. If you can’t understand why, then you’re ill-informed about human nature. I shall accept no other lover than Rhombur. That is not a subject for negotiation.”
The response of the Sisterhood was to send the first 'Guilt-caster' after her:
“You have always had a purpose to serve, but now I have another use for you. The Sisterhood cannot allow open defiance without consequences. Therefore everyone must see your guilt, and you must feel it. You must know it.”
“Never forget that you belong to the Sisterhood—heart, mind, soul, and flesh. You exist to serve. Contemplate that in your personal hell.”
So, she violated orders, but was then rendered catatonic and forced to obey them anyway, against her will.
Arguably, I suppose Sheena in 'Chaperhouse' counts as well, but that was closer to a Schism, breaking apart from the 'New' Bene Gesserit, than a direct violation of orders.