This sounds like the first book of the War Surplus series by Lawrence Watt-Evans, The Cyborg and the Sorcerors.
Slant, the Cyborg warrior, a type of spacefaring Robocop, has been ordered to kill the enemies of Earth and return with their weapons technology. The problem was that Earth had perished three hundred years before, but no-one had told the spaceship.
Slant does have his synapses bridged:
Slant's nervous system had been completely rewired, and the synapses bridged or eliminated, so that his reaction time was measured in millionths of a second instead of hundredths.
and he does have a bomb in his head:
The Command's method of ensuring the loyalty of its IRU cyborgs and making certain that
none of them fell alive into enemy hands was very simple; any attempt at surrender, or any sign of cooperation if captured, and the thermite bomb at the base of his skull would go off.
The ship does try to destroy the planet because it's programmed to wreak as much destruction as it can if its pilot (i.e. Slant) dies, and for some reason I forget the ship thinks Slant is dead. I think it's when the thermite bomb is removed, as the surgery involved also removes Slant's link to the ship.