Here's the thing. Evolution doesn't work that way. It isn't predestined. It's just a process if cause and effect. The fact if the matter us that they were there and could have helped but chose not to. We evolved too. We gave a responsibility to act when we can to help. They raised their hands up and bestowed upon evolution a mystical pre-determination as though it were a god unfolding a higher plan.
I'm not saying I agree, but there is a case to be made, and some well-known atheists have made it, that there is no freewill, and that everything is predestined.
But, more to the point, I can see the prime directove (in this case, before it was actually a directive) intent on keeping us out of the natural evolution that would haev happened, just as it did for the death of a species in Homeward.
We don't have to agree with the ultimate decision in Dear Doctor, but that doesn't make it stupid. It would have been stupid if both Archer and Phlox didn't think carefully about the decision, and moved on, but the whole episode was about a careful consideration about the meaning and implications of interference.
The point of the Prime Directive, the thing that makes it interesting for dramatic storytelling, is that you are supposed to remove empathy and emotion from the situations in which it would apply. Think about that.