Can't you find a set of quality lights that will fit back in to the same holes? That looks awesome and it's an excellent idea!!
EDIT- Best idea came actually from my wife (yeah, not typical to have a smart boating wife) Why don't you make a custom fiberglass housing to go around the back of the lights, then, just gel them over from the back side? So, even if the lights did leak, the water can only go behind the light itself and not into the boat. Like a fiberglass "Pocket" behind it.
-if not-
Might be a little expensive, but find a CNC metal fabricator who can put the exact size of those lights into a CAD program and mill yourself a set of light rings out of Aluminum, then, have it powder coated or even POR15 marine the housing. Could have it anodized also, but that's not usually the answer. We've had alot of stuff custom fab'd for the boat and it's usually not too bad. It's gotta be better than trying to fill holes just because of poor quality lights. Take a look at Pool lights also (Just for the design). Those things sit at the bottom of pools under intense pressure and don't leak. The o-ring, glass and bezzel on those are designed correctly and might help you make lights that work and don't flood the boat. Good luck, but stick with that look if you can, it's awesome!