Creating transactions should not allow creating dust.
At the moment, dust outputs are not checked for when constructing a new transaction. At the very least, the send should fail. A nicer implementation would show an error next to each dust output and prevent the transaction from ever being constructed.
Once #43 is done, the user could set a higher transaction fee, which could change the dust threshold. This is less surprising than modifying any fee estimation logic to use a higher relay fee just to accommodate a dust output.
My comment about using this fee to change the dust threshold is incorrect. The dust limit determined by a full node is not based on the transaction's actual fee/kB but the minimum relay fee used for the mempool's acceptance policy.
The only thing we can do here is display a nice error next to dust outputs, and perhaps inform the user what the dust limit actually is so they can fix it by sending a larger output.