Caretaker had been part of local politics for the last thousand years, but you see him as an external factor?
By that reckoning, if Janeway was to show up on Earth today and a couple native American Indians where to ask her to smash whitey who was overrunning their country she'd be all up for it? Removing a foreign alien influence disaffecting the proper land lords of America?
Ditto with the English in Ireland.
Ditto with whitey in Australia.
And goodness knows who she would side with over Jerusalem because Kathryn wouldn't be phased by who had the oldest if not cutest claim to the Holyland that her sense of righteousness can justly ply apart thousands of years of rebuilding their homes on the bones of the recently murdered?
Caretaker was part of the local politics just like the Romulans were in charge of Reeman space, of the Cardasssians were allowed to occupy Bajor because after 50 years the status quo had been accepted as just something that is, because the first movements originated before most of the current players were born.