The engine can throttle between 50% and 100%. It is true that even 50% of just one of the nine engines is enough to shoot the rocket back towards space. Which is why it can not hover.
But hover is not relevant. Hitting zero velocity at height zero is.
Let the rocket drop freely while continuously calculating needed thrust to hit the target velocity zero at zero height. Keep dropping until your algorithm says you need 75% thrust. At this moment you relight your engine at 75%.
Now you can do a control loop with feedback to vary the throttle between 50% and 100% with the perfect descent hitting 75%. This should be plenty to do the job.
In addition you have at least two other mechanism to help a successful landing. One is the braking by aerodynamic mechanisms that can be varied. Those might be more precise than engine throttling. Another is the landing legs. They will be designed to absorb hitting the ground at a small non zero velocity.