In my opinion, the fees being based on KB is makes multi-signature transactions more expensive while I think multisig should be encouraged somehow.
It would be even better if multisig transactions were actually cheaper. Just to push it's use.
Maybe a better solution would be a % of the transaction amount. It's also easier marketing if Bitcoin only charges 0.000x% per transaction while banks, VISA etc. charge x%.
If you want to avoid spam, a better solution would be hardcoding the minimum transaction amount instead of hardcoding the minimum fees.
So if you start with 50 btc, spend 0.1 and 49.9 go to a change address, you'll pay a % of 50 btw in order to spend 0.1 since the miners can't tell what the "transaction amount" is?
You can always (so far) send a no-fee transaction.