Not necessarily.
For example -- Eb says she broke the First Law, and they were hunting her.
But what if she had been framed?
Knew she was innocent, but that she was under a kill-on-sight order?
Alternatively, I (and others) suspect that the "Dinner Party" she had invited Eb to -- he one with the white King & Duchess Arianna (where she spotted that Eb & Maggie "fought like family") -- was likely a "Black Council" initiative, an effort to recruit Eb. And if she was inside the "Black Council," it is entirely possible that she knew (or had excellent reason to suspect) that the White Council was already too compromised for her to shelter safely there.
I'm sure that Jim could create other valid reasons for Maggie Sr. to be "less evil" than depicted, but unable to claim any sanctuary or safety with the White Council. We know our understanding of her to be woefully inadequate; both incomplete, and mistaken in (at least some of) the details.
Agreed about out lack of knowledge.
But...this is where Ockham's Razor cuts sharply. We don't have much hard data about Margaret, but we've had lots of hints and clues, and most of them point in the same direction. Eb said point blank that she had broken the First Law, and added 'among others' IIRC. Nicodemus has 'fond memories' of Margaret, and her ability to make her own simulacrum and project it into Thomas and Harry's minds suggests she knew the Denarians well enough to study some of their abilities. Thomas called her 'one hell of a dangerous witch'. Chanzoggorth said Hell thought they were going to claim her. Lea said that Margaret acted like Harry...at the very end of her life. Not before. Goodman Grey, IIRC, called Margaret a 'piece of work'. That from a half-Nagloshi. She was plotting something with Lord Raith, who is known for being a Solid Guy (that's sarcasm, son, as Foghorn Leghorn would say), and Aramina, who is Aramina.
Out of all the hints and clues we've had from people who knew her or interacted with her, only Stacy's version is at all positive (and Lea's a little, Lea said she started acting like Harry acts at the very end). All the other references have been negative. Oh, yeah, one other tiny good sign: apparently Martha Liberty had some kind of positive opinion of Margaret, or so it's hinted at one point.
But the overall thrust is bad.
OK, maybe she was like Harry, broke Laws but not a true warlock, complicated extenuating circumstances and so forth. But contrast their reputations. A lot of people, on and off the Council, think Harry is a dangerous menacing warlock or worse...but there are also a lot of people, on and off the Council, who have very high opinions of him, too. It's not hard to find people in the Dresdenverse who'll tell you that Harry Dresden is a stand-up guy and solid. If a lot of people hate, fear, and distrust him, a lot of other people hold him in high regard and respect.
In contrast, almost everything we've received about Margaret is negative.
So what's the simplest interpretation of the data, as William of Ockham would ask?
One possibility (and I don't necessarily believe it, it's a WAG): during her idealistic wild youth, she might have found herself in a situation kind of like Harry's life, breaking a Law or two in
extremis, and wrongly condemned for it. If she went down the wrong road after that, the twisting effects of black magic and bad company could have turned her into the Margaret we've all heard about.
Which might be part of why Eb is so worried about Harry's current activities...