She did break the rules that Traven set.
Rules that may have yet to have been enacted.
The Knights of the Lamp were enforcing the guild law, probably to bring her to a Mages Guild trial to determine whether or not to expel her. We don't know how long it was between when the ban was enacted and when it was discovered she was practicing necromancy behind the guild's backs. And really, if she went peacefully, the worst punishment they could enact would be expulsion.
They could have also just sent her a letter telling her to GTFO, or sent a representative of Traven to take over and/or keep a close eye on her. The fact they sent their private police force suggests that they were not going to be friendly, and were ready to be rid of anyone whom they thought to be a necromacer. In addition, because so many members were kicked off and joined the Worms/became pretty hostile, suggests that the Mages Guild was going to remove them by force, and forced them into a situation where they literally had to fend for their lives on a daily basis. Not only from ignorant and fearful peasantry, but also from fanatical "good doers" of the guild. Plus, many regular guys also probably became disenfranchised with Traven, and I doubt the half of the council that initially left were all necromancers, but most likely high level mages who became sick of the heavy handed regulations. And because of this poor treatment of them, the guild most likely caused many more of their former members to be extremely disenfranchised and ready to follow some leader who offered them salvation against their injustice, and throw down the evil the Guild caused in the face of "justice" and "being good."
His ban was unwarranted, and I find that it was the Guild that struck first with their heavy handed approach. Heck, I'd say (until otherwise noted) the founders of the College of Whispers were probably former members of the MG who found the heavily regulated rules to be disgusting, and made a deal with Titus to officially recognize them. And in return, provide magical research that would help the newly made empire from hostile forces and bring the empire back into a well educated state.