It was a shocking moment, sure. But, it wasn't a huge leap at all. Again, remember how he saved her from the Eagle? It's been fairly subtle but it's been pretty clear that he has been growing to care for this girl in some wa, romantic or not I don't know. In any event, I think doing it like this was for the best. It kind of shocked the reader as much, if maybe just a little less, than Netero and Zeno who had no idea of his changes.
Interesting thing to note is that there was no narration regarding Pitou's tears in the anime. I think I prefer that, as that specific part was more powerful in the anime imo. Otherwise, I like the scene pretty much equally between the two versions.