Well, it's sort of like ghosts, every time anything resembling magic comes up, the Doctor can prove that it's only science that the people don't understand. When Aleron starts to chant, though, the Doctor realises he made a mistake by mentioning it. He relaxes when Aleron comes back fairly quickly.

"I do what I can to help those in need. And we were talking about how I might be able to help you."

Or not, since he hadn't used his abilities much in Thedas beyond the animals. But it worked the same way on them back home, why wouldn't it work the same for humans?