Operating a gaseous fuel engine system includes determining a detonation level in combustion cylinders in an engine in the gaseous fuel engine system, comparing the detonation level to a detonation level limit, calculating a detonation error, and limiting an engine load of the engine to a derated engine load level based on a reduction to intake manifold air pressure (IMAP) that is performed responsive to the detonation error. The gaseous fuel engine system can be operated at a reduced, derated engine load, rather than being shut down, and permitted to increase in engine load level as detonation events clear. Related control logic and structure are disclosed.