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.