Yeah, the doctor has been portrayed as sympathetic; his motives for getting the belt even seem fairly pure. If it has some sort of enhancing effect, shouldn't that be shared with humanity? Shouldn't that be examined for the betterment of all?
Which is why I lean towards a charitable reading of his actions. He didn't realize that he has given her no identity other than stealing the belt, because he's come to value her for more than that. It's not like he's done with her now, she just doesn't have to do anything anymore. He's missed how much meaning she's gained from all the things she's done and how much she's grown in her journey. Also, that she's like... into the hero now.
So far, there's only one actual monster in this series: Dan. Which is why he looks like one.