The right decision depends on the condition of the whole roof, not simply whether one leak exists. A younger roof with localized damage is a different situation from an aging system with repeated failures.
Repair usually makes sense when
Damage is localized, matching materials are available, the surrounding roof is still serviceable and the repair can restore reliable weather protection.
Replacement becomes more likely when
Problems are widespread, the roof is near the end of its service life, multiple areas are failing, decking is deteriorated or repair costs are accumulating.
Ask for both options when the answer is close
When either path could be reasonable, ask what each option solves, what remains unchanged and how long the contractor expects the repair to remain practical.