People seem to forget that life dealt Maggie heavy blows from early on. Her mom died while she was a girl, and she had to grow up overnight as her father seemed to give up on life after a) losing his wife, and b) making his devil's bargain with Roger at Burke's expense. This made her a bit cynical and she had to learn to fend for herself, and the result is the gal we made met in Episode #1, who called Vicki a "J-E-R-K" for wanting to work at Collinwood.
What softened her? First, she found love in the form of Joe Haskell. Second, with Sam's revelation of what Roger did to him and Burke in '55-'56, a great weight was lifted from his shoulders and he stopped drinking. With that, Maggie was no longer burdened with having to worry about her old man 24/7. Life began to look brighter for her. Then Barnabas appeared, and she descended into that nightmarish "existence" at the Old House. That steely resolve which helped her exist without a mother and an alcoholic father came in handy- no matter what, she never gave up during her ordeal, though she was on her last legs emotionally when Sarah appeared and helped her out of her cell and back into freedom.
Of course, she was deeply traumatized by those months of capture, and in the long run Julia's hypnosis did Maggie a favor- it enabled her to go on living. Like the survivor of a war or disaster, she now had a new appreciation for life and her earlier cynicsm was gone for the most part. Remember the scene in '68 when Maggie told Vicki that she and Joe were planning to marry soon? That would've been unthinkable for the hard-luck gal of '66 we met at the Collinsport Inn!
There were still traces of the "old Maggie" still left in her as she confronted Quentin's ghost to save David in 1969, and as she became suspicious of the going-on at Collinwood as the Leviathans ran rampant. In her final scene in the series there is still evidence of the inner strength that helped through her early years. Sebastian may be driving her off to Wyndcliffe, but in her heart of hearts she wants to go back to Collinwood to help Barnabas and Julia save the children from Gerard's ghost. The Collinses have become her family, and that's why she says to Sebastian if they continue on their journey to Wyndcliffe, she may never see anyone from Collinwood again. What she really means is "If anything happens to the Collinses and Julia, I'll never forgive myself for not being there with them when they needed me most" Very compassionate, and very mature- beyond her years.