I can see the GUI not allowing a less-than-CENT to save fat-fingered users from themselves, but I think the RPC should allow it; at the very least it makes it possible for a kind of grass-roots movement to arise between miners and people generating transactions so if we start seeing a lot of transactions with less-than-CENT-per-kbyte-fees then that's a really good indication the default definition of "free" needs to change.
And now that the RPC and GUI allow full-precision amounts for send/move, there is no problem with "I got 50.000001 bitcoins from mining, how do I send ALL of them?"