However, there should be some metrics and heuristics that take care of
this problem. Notably the dev consensus (sans you, Mike :)) seems to
be that uneconomical outputs should be made non-standard.

I think that patch is ok as it doesn't really have any fixed concept of what is uneconomical. But I haven't thought about it much. As Gavin says, there's an obvious backwards compatibility problem there. It should probably wait until the payment protocol work is done, so the major user of micropayments-as-messages can migrate off them.