I'm sorry, what's the problem with changing the limit in IsStandard() back to 80 bytes? I have yet to see any argument for why 40 is better than 80, and using the latter value would benefit everyone involved immediately.
For relay, probably no immediate problem.
For mining, it encourages spam.
For long-term, it's unnecessary.
Edit:
Except that relaying transactions which will never be mined is currently exploitable. So either that would need to be fixed first, or the relay needs to be more intelligent and only relay Counterparty transactions the same way miners would mine them.