The dialogue in the first episode of Star Trek: Voyager almost explains this.
Tuvok: Any action we take to protect the Ocampa would affect the balance of power in this system. The Prime Directive would seem to apply.
Janeway: Would it? We never asked to be involved, Tuvok... but we are.
Is "being involved involuntarily" an exception to the Prime Directive?
The array would have been destroyed anyway... except that Voyager instigated a battle with the Kazon that damaged its self-destruct capability. Janeway was simply fulfilling the wishes of an advanced species that Voyager had already interfered with.
The rules concerning the prime directive basically boil down to this:
None of these rules were (technically) broken. The reason for this is because they weren't (technically) involving themselves with the Ocampa but with the Caretaker(A Nacene who did meet all the criteria for interference from Starfleet to be allowed). The Caretaker accidently destroyed the ecosystem of the Ocampa homeworld making the nature of their disaster fall outside the reasonings to them not being allowed to help (Seeing it was neither natural or self inflicted).
The Caretaker wanted his station destroyed so it could not fall in to Kazon hands and although this would ultimately be beneficial to the Ocampa, the destruction itself would help a warp capable species fix the problem they caused by not following rules similar to the prime directive.
This isn't the only or first time Starfleet officers bend the rules or interpreted them a bit loosely to make their decisions.
The Prime Directive itself is never fully stated (probably so it would allow for small additions/retcons by the writers). Episodes the prime directive are notably mentioned and explained are:
Directives are fine but everyone knows exceptions to rules always happen. The Prime Directive is a guideline to be sure but rigid-mindedness in the application of any rule can sometimes create undesirable conditions.
Captain Janeway's mission was to apprehend the rebel Maquis. It got complicated getting pulled into the Delta Quadrant. By deciding to fulfill the dying request of the Caretaker, Captain Janeway involved the Federation in a situation between alien affairs. Captain Janeway knew very little about the Ocampa, the Nacene or the Kazon. No treaties existed. Making decisions in this manner begs for mistakes. Janeway agreeing to follow through with the Caretaker's request presumed it would be in the best interest of the Delta Quadrant aliens if she destroyed the array station, but again, no treaty existed to support any of them. Janeway could not make such a desicion unilaterally. She didn't know what these races were really like.
After completing her mission, Capt. Janeway should have secured a pathway back home for the safety and welfare of her ship and crew.
