What are the differences regarding the first choice in starcraft 2?
Solution 1:
The doctor wasn't only trying to save the colony but was also trying to save herself. She turned out to be half-infested already and the cutscene after the mission shows you dealing an infested version of her.
I didn't find any noticeable impacts on the decision I made aside from the bonus research though.
EDIT: Didn't notice this one. Apparently the reward is visual. WIKI
For Safe Haven (siding with the terrans) you get a banner from the refugees.
For Haven's Fall (siding with the protoss) you get a commemorative plaque from Selendis.