It's pretty standard practice to grind the tips of the valves. Usually it is done with minimal material removal to clean up the wear marks on the tip, but can also be necessary to correct the valve stem height in some cases. How much can be taken off depends a lot on the valve construction. Some valves have a thick hardened cap on the tip that allows quite a bit of material removal as it is part of the engine design. Others are simply case hardened and have minimal allowable thickness to grind off.
The other concern with grinding the tips too much is how that will affect the protrusion from the spring keepers and cap. Too little and the rocker or follower cap can end up pushing down on the keeper or spring cap which can in a worst case situation cause the keepers to release the valve and destroy the engine. Looking at the picture of your valve, my guess is this maybe the bigger issue for you. Second problem with seats that are too deep (aside form a whole lot of problems with flow dynamics) is the spring length will need to be corrected with shims. As the stem protrudes more above the spring seat it causes insufficient spring tension which will affect valve closing rates and may result in early valve float.
Bottom line, my concern would be that if the valve seats are so deep that you have exceeded the working range of the hydraulic lifter, you have seats that need to be replaced as the proper corrective measure. Anything less would be a bandaid solution that may have a cascade of consequences. You need to verify what the design and engineering tolerances of your engine allows for in this condition.
