Well isn't the minimum fee 0.0001/KB

Thanks for your information on this part, though.
No such thing as minimum fee but the default relay fee is 0.00005BTC/KB.
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.
Not an issue. We get spams that is much bigger than that. If the payment is made every week, the transactions would only occupy a total of 2/168MB. The gambling sites produces spam on a much bigger scale.
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,
Wouldn't you be introducing spam instead?
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.
Possible but it isn't that important to reduce the spam from these kind of transactions. Actually, I had people who had change of less than 2730 satoshis and I had to walk them through to solve this. It can happen more if its 54600 satoshis.
The reason for the dust limit to be lowered was because of the increasing price. It would be quite dumb if you aren't allowed to send 0.5USD across the network. Segwit would likely help with the block and transaction size and potentially reducing the impact of this issue.
Aren't most faucet sending payments through online wallets like Xapo?