I always thought the Prime Directive and the need for exploration conflicted. Honestly, any time you even enter a sentient beings system there exists a chance for contamination. No matter what precautions you put in place.
See: The Omega Glory
or Who Watches the Watchers
Plus, you are actually violating others territory in the name of exploration. The Federation has decided that their need for knowledge outweighs a cultures right to know what is happening on their own planet.