That would certainly explain why we didn't see Evil Nina during Seasons 1 - 3. But it does beg a question, though: If there was no Bell and MD in the alt-verse, then how did alt-Nina end up with a bionic arm?
The whole thing about the alternate universe, when you think of Walternate and Bolivia, it's a tougher world. [Fringe showrunners] Jeff [Pinkner] and Joel [Wyman] said that in this world there was no William Bell, there's no Massive Dynamic. So Mean-a has the same intelligence, ambition, drive, yet she's thwarted her whole life, until Jones shows up and says, "Hey you can be part of this. Oh by the way, we're going to cut off your arm." And she's desperate enough to be part of things that she says yes. It's a much more craven quality than our Nina, who keeps things really close to the vest.
Link to her interview:
http://www.tv.com/news/fringe-q-and-a-blair-brown-on-this-weeks-incredible-episode-27935/