A few thoughts. I obviously think about this a bit, since that's my post that Joe's riffing off of, and I just blogged here recently on the topic of evil PCs.
1) The whole "what do you mean by hero?" discussion is, I think, a bit of a tangent. Sure, there are esoteric definitions of the word hero, including all kinds of stuff related to Greek stories and whatnot, but do we really want to go there? I think we all know what the most common relevent definition of hero is in regards to D&D.
2) I think the heroic paradigm was pushed during the era of 2e, when there was a real desire by TSR to not be percieved as "that Satanic game" or whatever. Since then, that emphasis has faded. Plenty of the novels do not feature heroic (necessarily) protagonists either, particular in the Eberron novel line. So, I disagree with your perception of emphasis on heroics. If there is one, it's very weak and very subtle, and certainly there's nothing inherent in the game that forces or even necessarily encourages you to be a do-gooder.
3) How does a streamlined alignment system make it more convenient to not be heroic? The clunky nine point alignment system has a much older vintage than 3e or even 2e, which goes back to your mercenary PCs days.