While it's possible for any individual to put a price on just about anything, it ain't always easy (as you just explained). We've decided that it's the government's responsibility to help put a price on some of these ineffables -- air quality, etc.

For a well-functioning market that doesn't get bothered by protests and other political machinations, the government needs to provide an easy mechanism to pay for whatever it is you care about. Any market which is restricted to folks who can afford high-cost lawyers and custom legal contracts, that market will be inefficient. Saying, "put a building-height covenant on it" in effect means "let's spend money and time on political advertisements and protests so neither of us are happy."