Well, miners can ignore transactions that have small fees or no fees. If there were not enough space in a block for all outstanding transactions, the transactions with the least fees will just be ignored.

So, there is an economic mechanism already in place to make sure dust transactions are paid for.

So that's not the problem that's being addressed.

EDIT: Well, actually, it's a "tragedy of the commons" situation. Having tons of dust transactions is seen as bad for Bitcoin (for reasons that are not yet 100% clear to me). So the devs think there is a need to dis-incentivize that. But the economic mechanism I explained above has not yet kicked in, so right now, you can make tons of dust transactions without having to directly pay for it. The burden of storing those small outputs for all time then falls on everybody who uses bitcoin.