Well isn't the minimum fee 0.0001/KB

Thanks for your information on this part, though.
It isn't an issue. Is everyone going to spend it at the same time?
Maybe not, but the whole blockchain will be finally spammed by 2MB worth of these transactions (every week) and stored into all computers with full node indefinitely.
The withdrawal threshold for most faucet sites is actually quite big enough. Theres a huge problem with increasing the minimum output size to that amount. In a normal transaction, there is likely to be change sent to the change address. Many a times, the change output is very low. Penalising them wouldn't make sense.
Even 54600 satoshi worths only ~0.5 USD now. They may use another input, pay a slightly less fee (if the change amount would be close to 54600 satoshi), or give the change as fee too. In realistic bitcoin transactions, a change of such low amount would occur rarely.