Agree with one addition: when deciding the right way of proceeding we must also take into consideration, that we may not have the full set of information to carry out the decision. Situation for example: we see two men struggling on the street, we help the one who seems to be the victim, and then it appears that our “victim” was a thief who stole the second man’s wallet :) Yes, it’s an edge case, but edge cases best show the complexity of moral decision making. As you wrote, PD is and should be a general rule and a help to make the proper decision in situations without enoug information or morally ambiguous.
Yes, evolution doesn’t have a will, but it’s a natural process that just goes, and speaking about “will” here is just a some euphemism for not wanting to interfere with natural process. The episode was supposed to really show the problems and dillemas that led to form the Prime Directive, and aside of what we think about Phlox decision, it does it’s job.