I agree this is not inline with the original intention of the software, but I don't think there's a way around it. Miners will do this eventually, even if most of them aren't, yet. Let's not pretend they won't.
I'm not intending this as a point for or against this patch, but I reading this set me wondering how many of the other assumptions we'd normally make about Bitcoin would still hold given this (fairly reasonable-sounding) idea that a majority of miners will be acting purely out of economic self-interest, regardless of damage they might do to the Bitcoin ecosystem.
One assumption that immediately falls is the idea that Bitcoins are censorship-resistant. If miners are all acting in their own rational self-interest, I can pay miners to blacklist transactions coming from your address. If you tried to spend, I'd tip any miner who creates a block that doesn't include your transactions at a higher rate than their fee. If they do manage to get into a block, I can (for a greater cost) also tip people for ignoring that block and building on another one.
If I'm trying to do this on a large scale - say I'm the DEA trying to interfere with the flow of money to drug smugglers - I can keep that taint going on all the way down the chain through future spends, so that once you take money from a drug smuggler, that money will be forever less valuable than other money. If you don't want to receive dud money that's hard to spend, you're going to have to check for the taint as well. I can run a convenient web service so that you can check for black-lists, and also white-lists of people who have confirmed their identity with me so you can be sure I won't bribe people to taint their coins. Hey presto, everybody is cooperating with me to do AML checks...
This wouldn't fly now because miners are
a) Decent people, not purely rational economic actors.
b) Fairly [shock horror] centralized, which makes them resistant to a Tragedy of the Commons. BTC Guild and Slush won't cooperate with my evil scheme for fear of damaging the future of Bitcoin, which costs them more in the long run.