I tend to think this is why prime directive situations have a way of ending up with the crew debating strenuously about whether it applies to the situation, whether it really might be best to just fly away and let the disaster happen, or whether Starfleet was actually destined to intervene, etc. Most people probably don't really like the prime directive, they're in Starfleet because they would prefer to help everybody if they could.

But there's always a certain arrogance in assuming they know what's best for a planet they just discovered. Starfleet is powerful enough to impose their will on many situations but it is also spread thinly enough that they might not make second contact for a century. Plus there certainly are bad seeds in the organization who would gladly take the opportunity to become a dictator or turn a planet into Nazi Germany. So Starfleet has decided they need to prove to themselves (and possibly to a future court martial) that the right decision really is to change a people's way of life, and not to just fly away. So they'll test out all these possible arguments on each other.

The prime directive does often need to be challenged. Its purpose is to try to make sure that altering a whole society's destiny never goes unchallenged.