I agree with you David. I think rather unconstrained covenants are incredibly useful and important. Yes you can burn coins with them, you can also permanently limit the usability of certain coins (which is less destructive than burning them). But as Jeremy said, people are free to burn their coins. People would also be free (in general) to reject coins encumbered by weird government provisions or unknown provisions in hidden scripts. A person/wallet shouldn't accept coins encumbered by scripts it doesn't recognize.
Even if 99% of bitcoins became permanently encumbered by weird covenants, the other 1% could still be plenty of bitcoins to run the economy, because of its potentially infinite divisibility. Losing these coins, or someone basically turning them into altcoin-like bitcoins shouldn't be a concern really. What's the risk exactly? That people will be forced to take these encumbered coins? A government can already force people to take whatever altcoin they want to force on people - covenants don't make this worse.
Shinobi asks: "What if you extorted users with your 51% attack to move into those?"
Well, you could do this anyway even without covenants existing already. The 51% attack could simply extort people to use whatever rules they want just as easily (which isn't to say that easily - most users would probably refuse to be extorted in either case). So I don't really think this is very valid.