Wouldn’t that require everyone to resync the chain, though?
I think simply using txout proofs is fine, given that it is extremely unlikely that someone created a dust UTXO in a 1MB transaction which they want to spend someday after it would expire.
Also, people would have plenty of time to consolidate such dust outputs before the proposal would activate, so I think it is fair to shift the responsibility to those users who want to keep using dust outputs which are a significant burden for the whole system as they are indistinguishable from the spam that makes up half of the UTXO set.
Pretty much every regular user wouldn’t notice the change at all, because even if your UTXO is worth only $5 today, it would remain untouched for 100+ years.