Adding a couple female guppies might work to distract him. Granted you might have some baby guppies, but the other fish will probably make short work of them. Although I agree the betas could potentially cause problems and might be the ones picking off their eyes.
Also, once you get the problem that caused your neons to die figured out, increasing the school to 6 or 8 will help them feel more secure and them being a larger group might make the guppy less inclined to chase them.
Also something to consider is that the ones that died could have died from other reasons, and the eyes got picked off by the guppy or betas after they were dead. It's not uncommon for fish to pick at other dead fish.
How long has your tank been set up? Is it cycled? What are your ammonia, nitrite and nitrate levels?