So, these seem to conflict slightly, to me at least.
You consider the PCs deciding to go do something else a campaign ending issue while at the same time not choosing to step on their player agency by starting them in a different part where things are already in media res?
Did you (or the GM if it was not you) tie the PCs to the events beforehand, so that there were in character reasons for them to value going to that city and helping?
Looking to be supporting player agency and also "you dont make certain choices and I decide the campaign is over" seem to be more or less opposites of each other.