Alright, I'm going to sidestep the whole was Maggie evil for most of her life or not debate, as I think that we are a bit short on evidence to reach a conclusion, in favour of trying to set up an approximate Maggie Dresden timeline based upon what we know in order to clarify some of these issues.

According to the DF timeline thread, Maggie is over 100 years old when she becomes involved with Lord Raith.  Thus, as Thomas was born 34-35 years pre-SF and she was presumably involved with Lord Raith at least a couple of years before his birth, let's say that she hooked up with Raith 37-40 years pre-SF, as, if Raith is a WC vampire, then I would assume that they were having a lot of sex.  So, as a ballpark figure, let's say that she was born around 150 years pre-SF (I know that you said it should be more like 180-200 years per-SF AA, but I'm not familiar with the WoJ you are citing).

~ 150 BSF
Maggie born

~ 140 BSF
Maggie manifests a talent around the same age as Harry according to WoJ, so probably she's 10-12 years old.  Presumably, as she was was Ebenezar's daughter, he finds out fairly quickly and soon takes her as an apprentice.

~ 135-130 BSF
Maggie's apprenticeship ends.  Feeling resentful of Eb's strict training, she sets off one her own.

Between 130 BSF and 50 BSF
At some point in this period, Maggie gains knowledge of the Ways surpassing that of any other living wizard, so she is probably spending a lot of time there at some point.  If her abilities were well-known enough that people were calling her Maggie LeFay, she presumably had them at least 10 years before she went warlock.  most likely, if she came to be widely known by this name, she had this ability far longer (maybe by 100 BSF).  In this period, she is not being hunted by the wardens.  We don't know whether she is breaking the laws without anyone else noticing, but, at the very least, she is reveling in what the council considers grey magic, including (probably) things like summoning demons, as Chaunzaggoroth says that "Many in the underworld were … familiar with her."  To be honest, she might also been involved with Raith later in this period, as I am not aware of any source which tells us when their relationship began, so take the later date with a grain of salt.  According to Luccio, she advocated for change in the White Council during this period, wanting the Laws of Magic to embrace concepts of justice.  Presumably she was also associated with DuMorne in this period, as, since DuMorne was a known associate of Maggie and a warden, they must have met before she was a fugitive from White Council justice.   

~ 40 BSF
Maggie becomes involved in a relationship with Raith.  As I have said, this date may be off, so take it with a grain of salt.

Sometime around the beginning of Maggie/Raith and before Thomas' birth (so before 35 BSF)
“A dinner. Maggie—my Maggie—asked me to a dinner. She’d just taken up with that Raith bastard. Arianna was there. Maggie didn’t warn me. They had some scheme they wanted my support on. The vampires thought I was just Maggie’s mentor, then.” He sighed. “I wanted nothing to do with it. Said she shouldn’t want it, either. And we fought.”

Maggie is involved in some sort of scheme with Raith which Eb refuses to support and discourages (this could be something to do with the Black Council, although that is, of course, speculation).  It is worth noting, however, that as Eb is not under orders to kill Maggie during this period, she cannot have openly broken the Laws of Magic yet (although, as noted earlier, she might have done so secretly).  She might also have done terrible things prior to this point which did not violate the Laws of Magic, as Chaunzaggoroth says that "her coming was awaited with great anticipation."  Again, this is just speculation, as she might have not done anything truly horrible until a little bit later.  We have scant evidence one way or the other.

34-35 BSF
Thomas is born.  Maggie imprisoned in the Chateau Raith.  Most of the council believes that she has run afoul of something in the NeverNever according to Luccio (as Luccio says that she disappeared for 4-5 years, she cannot have been imprisoned too long before Thomas' conception).

29-30 BSF 
Maggie escapes Raith when Thomas is about 5 years old.  According to Eb, "she turned away from her previous associates-including Justin DuMorne. After that, nowhere was safe for her. She ran from her former allies and from the Wardens for perhaps two years. And she ran from me. I had my orders regarding her as well."

28-29 BSF
Maggie meets Malcolm Dresden.

27-28 BSF
Maggie is killed by Raith.


Thinking about this timeline, two important points occur to me.  Firstly, if Maggie redeemed herself, then she was only doing so in those last two years when she was on the run.  Moreover, as Eb "had [his] orders" regarding her in this period, but was free to meet with her when she began her relationship with Raith, Maggie must have only begun openly breaking the Laws of Magic while she was with Raith (and before Thomas was born, as the White Council did not know where she was after Thomas' birth).  According to Eb, "she was guilty of violating the First Law, among others," so Maggie must have been a pretty busy law breaker while she was together with Raith.

Also, I know some people consider Luccio's testimony suspect, but I think that this timeline is consistent with everything we have heard from all the various sources of information on this subject.  Please correct me if I am mistaken.