The real mole is a good choice - probably the sweetest character in Charleston. And, my sweet Lord, it's sweet Lourdes! Which is not only a nice surprise, but makes sense in retrospect. Before she was taken over by the alien worms, she was a good medical assistant to Anne. This season, especially with Anne out of the picture, Lourdes has apparently become a highly effective, full-fledged doctor. This transformation is more explicable if due to alien help.
And that leads us to another likely consequence of Lourdes' conversion. She worked daily with Anne. She examined Anne to make sure her pregnancy was proceeding well and her baby was ok. She easily could have drugged Anne at any time. Any of which would have given Lourdes ample opportunity to introduce alien DNA into Anne's developing baby.
So we have an answer about how the hybrid baby came to be - better than Tom was somehow infused with alien DNA when he was on the alien ship a few seasons back. But given the propensity of Falling Skies to pull aliens out a hat, we may yet not know the full story of baby Lexi's conception, and we certainly don't know what's been happening with her since she and Anne left Charleston. How quickly, for example, is Lexi growing up?
Looks like good viewing ahead in the concluding three episodes of this season of Falling Skies.
And see also Falling Skies Returns ... Falling Skies 2.6: Ben's Motives ... Falling Skies Second Season Finale
And see also Falling Skies 1.1-2 ... Falling Skies 1.3 meets Puppet Masters ... Falling Skies 1.4: Drizzle ... Falling Skies 1.5: Ben ... Falling Skies 1.6: Fifth Column ... Falling Skies 1.7: The Fate of Traitors ... Falling Skies 1.8: Weaver's Story ... Falling Skies Concludes First Season