Let's note in advance that to consider this matter intelligently requires a mix of fact, speculation and conjecture, but I'll take my best shot.
Though it was a popular fiction of the time, I also don't think that the switch to alternate break had anything to do with trying to slow down Allison and Karen. The real reason that many of the women came to think that nine ball was unfair without alternate break was that the men, with whom many of them practiced, had come to feel that way.
The men came to feel this way very early in this decade, when use of the Sardo rack made it, in the eyes of many, way too easy to make the wing ball, and two matches explain, more than any others, why they came to hate winner breaks. Anyone who attended either will remember them well.
2000 BCA Open: Semifinal Archer vs Immonen
Archer got to the hill before Immonen even shot, and in the final rack, Immonen shot but never attemtped to pocket a ball, leading to a 7-0 whitewashing. It's the only pro level tournament match I've ever seen in which one of the players never attempted to pocket a ball. I chatted with Mika just after the match and he was geniuniely disgusted, feeling he'd been to denied a chance to win by the rack itself. It was the last BCA Open to use winner breaks.
2001 US Open
This one was another freaky one, and the victim was, once again, Mika Immonen. Corey Deuel won the final in a 13-0 shutout, using his break to control the match. He didn't break and run all the racks, but by making a ball every time with his soft break, he usually gained control of the table. It was another match in which the break itself made the playing field seem unfair. Of course, the latter part of the decade would be much, much kinder to Immonen at the US Open!
These two historic matches probably did more to popularize the call for alternate break in men's pool, and sure enough, alternate break (and/or use of the break box) went into greater and greater use in the aftermath of these two matches, which many thought to have been critical samplings of the problems that can come with winner breaks.
So What About the Women?
It should be noted that Karen Corr, just like Corey Deuel, developed and mastered a very effective soft break with the Sardo rack and Karen won some of her WPBA matches with the same kind of suffocating style that Deuel had been successful with. While the women had, in my opinion, already been advised by their male pro friends, to consider alternate break, Karen's success with the soft break earlier in this decade may have been the clincher. Even after the change to alternate break, Allison and Karen conitnued to win lots of titles. More recently, it is clear that alternate break has not slowed down the good breakers on the WPBA. Two of the best five breaks on tour today belong to Ga Young Kim and Jasmin Ouschan, who have combned to win the last five tour events.
In WPBA Play
If you're looking for the change that put and end to Allison and Karen meeting in, what seemed like, every final in the middle part of this decade, look no further than the change from true double elimination (up to the final match) to double elimination down to sixteen, followed by a redraw and single elimination for the last sixteen. The result was some new faces in the TV matches.
In Conclusion
I don't think that alternate break makes much difference in WPBA play. Ga Young, Jasmin and Xiaoting were the three best in 2009 and now hold the top three spots in the rankings, and I believe this would have been the case with or without alternate break.
That is my perspective, anyway.