The way I understand it, the Prime Directive was conceived not as a practical tool to protect alien societies or the Federation. The principle idea behind it is that as a whole the Federation does not want to take on the burden of playing God. Even though the UFP has shown no evidence of subscribing to theistic ideas it does recognise the inherent risks of hubris. Even though the Federation is exceedingly powerful from our point of view it is a long way from having the answers to everything. As a result, it likes to preserve the status quo when the consequences cannot be easily predicted.
It's similar with the laws on genetic engineering and technological augmentation. Federation society likes to preserve the fundamental identity of its species and cultures. Even though, these alterations would have huge immediate benefits they do have the potential to destroy the human condition and the essence of our identity. So even though the Federation COULD do this, it CHOSES not to. Because the consequences could be far reaching, uncontrollable and destructive.
So where do they draw the line with the PD? As far as the different series go, it seems to depend and the PD is applied with varying degrees of flexibility, as we all know. But the fundamental policy that starship crews should not hastily interfere in complex alien problems is sensible and wise and prevents the Federation from overeaching itself and causing more problems than it is solving. However, ignoring calls for help from alien societies that are in peril and have invested into genuinly seeking assistance from the galactic community is rather harsh. To me these episodes feel like false dilemmas because they exceed what the PD is really intended to achieve.