That's one risk you face when using a static Bitcoin address.   If your service gives a unique address per payment there is less chance of this being a problem.  But someone could repeatedly send spam-like amounts to inflict pain on the recipient.  A coin selection method that ignores amounts under a certain threshold when otherwise including them would increase the fee would neutralize that threat.

The only ones complaining about it so far are those who are getting the dust spam from their losing bets from SatoshiDICE, so that is self-inflicted pain.