You could make access to the base portable, by requiring the use of a portal stone or the like. The portal could take something like an hour to safely unfold, and critters can just walk through it to reach the homestead. That would prevent it from being an get-out-of-jail card, but make the base accessible most of the time. Narrative tools, like anti-magic zones, imprisonment, damage to the portstone, or a particularly sullen companion arc can also be used to cut off access if required.