Sure, allow contracts to be signed, where if a condition is violated then a penalty can be paid. But here? There's no one to buy off to relax the constraint. It's held in perpetuity by the dead hand of the past.
To put it another way: there's a property right here (in that setback) that is just sort of floating in the air, not owned by anyone alive. That makes it untaxable, when all sorts of other property is taxable. It should be possible for the city government to condemn that "property" and then change the covenant. They wouldn't even have to pay anyone, since there's no owner.