Why did he hesitate? The damn thing was trying to kill him and was tossing cars around like nobody's business, nowhere in the previous scenes was there any indication that he would have remorse for the thing, the bitch just said he was a plant god nothing more, she didn't say it was the only one of its kind until after Hellboy hesitated. And then the reaction of the people nearby was just plain retarded, there was hardly any indication that people hated him or anything, in fact it seemed like they liked him during the whole tooth fairy incident, and now all of a sudden they hate him and they think he hurt the baby for no fucking reason. What the fuck? The movie just felt slow to me due to all the unnecessary dialog that was badly executed; they're actions just seemed implausible.
As an aside, i know that some of us are all into this whole sacrifice the world for the one you love blah blah blah, but i don't quite think that sort of message is very noble. I do believe there are approximately 6 billion other humans on the planet who would very much like to keep existing regardless of your detriment.