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.
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.
Prime Directive or some sorts of regulation regarding contacts of advanced technical cultures with those less advanced is a necessity for a number of reasons. Of course, this is not an easy issue, as it touches so vague and fuzzy concepts like morality. I think there are some episodes that clearly show why it is needed, and some others why from our perspective it is morally ambiguous to say the least. For starters we should take a look in a rule that was stated AFAIR by Arthur C. Clarke: Any sufficiently advanced technology is indistinguishable from magic. This takes into consideration that lesser developed societies will have trouble to comprehend that some piece of technology is not something supernatural, but completely understandable and “normal thing” which poses the risk of the “higher” of two civilisations to pose as simply gods. TNG episode “Who watches the watchers” is an excellent example of this. “Devil’s due” is a second example that comes to mind, or the “Patterns of force” TOS episode. We even have real life examples of post WW II cargo cults in the pacific (also referrenced in “Star Trek: Into Darkness”, although very naively and simplicisticly, when primitive culture drops their sacred texts and starts to worship the Enterprise). In this view Prime Directive is a safety mechanism that tries to circumvent this problem: let the lesser-advanced cultures develop themselves, and when we see they have the capacity to understand complexity of our technology, or develop the technology and understanding at least somewhat comparable to our own, we can risk a contact without the risk of destroying the culture whatsoever.
Then there is a moral aspect of the PD: sometimes adherring to the PD will cause us to think if it is moral to not to interfere. Example is the aforementioned “Star Trek: Into Darkness” or the infamous Enterprise episode, where Phlox doesn’t treat part of population on some planet although he has the capacity to do it. This is problematic as we have problem with defining morality ourselves. For example the issue we generally agree that killing is objectively morally wrong, BUT we see some situations where it is somewhat of a necessity or it is “lesser evil”. But the issue is who should decide what really is this lesser evil? Then we come into the ominous trolley problem: how to decide who should live and who should die? It’s easy to condemn Phlox for genocide, but the complexity of the situation on that planet was far greater than just giving or not giving the cure. The valid question here is: who are we to decide? Why OUR set of moral rules is better then other moral set of rules, and why we should have the burden to take arbitrarily the decision for someone else based on OUR rules? Prime Directive is something of a workaround for the trolley problem: when proposed with this kind of situation we simply step back, and avoid making decision. Avoid “playing gods”. We can argue if this is morally good option, but let’s be honest: as a species we can’t even agree on a basic set of objectively moral set of rules for ourselves, how can we then impose such rules to others?
The best way to sum it up is a quote from “Donnie Darko”: It’s not that simple! :)
Live long and prosper
It would be pretty cool to see some episodes on some non Federation rase (like Cardassians or something) enslaving newly discovered civilisation.