Don't quote me on this, it's been awhile, but as I recall Phlox was basically supposed to be at odds with Archer over the situation. Instead of them both shaking hands and being cool with genocide. Archer was supposed to want to save the people and Phlox would be holding himself to the equivalent of a prime directive. (Not in so many words.)
Originally, 'Dear Doctor' was supposed to end in a different manner. "The ending that had initially been created I was fairly comfortable with. But the head of the studio suggested some revisions on the ending. What do you do? I wasn't as happy with the revisions, but it's not my show, you have to sort of adjust, even if sometimes it does seem a bit of a contradiction in terms for what your character is supposed to be about."
So how did the ending change? "[In the original version,] in this crisis of conscience, the Doctor essentially does something that violates the standard issue hierarchical obligations of a crewmember to his captain," he explains. "In effect, he makes a decision that's rooted in 'I've got bigger fish to fry,' rather than honoring his captain's wishes. The network essentially felt that no, it was important to essentially make sure that everyone was here to support the captain's decisions. Personally I thought, 'Well, I think you've kind of lost something interesting in this potential tension.' But, that's not my call."
Although disappointed, it's important to note that Billingsley doesn't have a major issue with this. "Everybody's got so many different agendas," says Billingsley, "and I can appreciate that one of the things they want to do - especially in the first season - is to really do whatever they can to support the idea of the captain being a very strong, and in control person. If they feel they undercut that in any way, they get worried. I understand that, but at the same time I think some of what makes the show - what makes any show - so interesting, is creating some of the tensions that exist between the characters."
One of the things I really dug about the 'Dear Doctor' episode were the scenes where we did come in to conflict, and that's why I was kind of wishing they hadn't had to undercut that tension, as it would have been an interesting thing to build on in following episodes."
- John Billingsley
At the very least, this would have been an improvement, because we would have gotten something out of it other than a pat ending. Namely, some good conflict between Archer and Phlox that would have (had the writers made use of it that is) resonated throughout the following episodes. Something potentially