I also believe Dr. Thad didn't have as much freedom of choice as he thought he did about the decision. I thought the story suggested quite strongly that Suzanne was correct in her belief that the passengers change the way their hosts think.
While I think this could be likely, a worse alternative is that he is not being controlled at all. This leads to alternatives that his actions come out of prejudice and personal decisions. There are plenty of examples of people enforcing their beliefs on others, as a way to both control others and to validate one's own opinion. This can be seen throughout the history of Native Americans dealing with Europeans as they used words like savages to belittle them and at the same time enforcing conversion on them.
His change in mind is common to belief changes, where someone makes a personal choice to go against their previous beliefs. Many times the people who come to a new belief system are the most fervent to defend those beliefs. When Dr. Thad takes the patient out to the graves, he thinks this would impress her, which it did not. He is angry because she doesn't see his view of the situation, which leads to his actions.
In fiction, we like to think there are forces that create evil, that we are not responsible for bad actions, but they are caused by agents of evil. It's much harder to deal with the reality that we ourselves can be evil, for all the right reasons. Dr. Thad justifies breaking his word to his patience in that he is saving them. He doesn't realize that he is repeating the mistake he made when he forcibly removed the symbiote from the previous person. He is deciding for other people what they need, not really considering the patient, as his father taught him.
It would really be interesting to hear his thoughts when he decided to remove the symbiote, as I don't doubt it would be a similar stream of thought.
Wonderful piece that can have so many interpretations, and make one think.