That tree thing didn't respond to Snow while she was preggers with Emma.
But she was able to go through the cloaking spell to get to Glinda while preggers with baby Bae. I mean Neal. And it's said over and over that Zelena had to have THIS particular baby.
Is it only non magic babies that can be pure, innocent souls?
No two babies are the same. It was Emma's destiny, even as a fetus, to either be an epic hero, or an epic villain (likely at least partially caused by Rumple using that potion on the Dark Curse scroll). Baby Neal doesn't seem to share that potential.