I'm confused. Are you or are you not notifying your customers of the added expense of supporting IE6? If you are, then I don't see how your method differs from what is stated in the post. No one is making their client "feel bad" about a business decision. Whether or not they do is more a function of how that unfortunate news is delivered, or perhaps whether or not they irrationally view IE6 support as mission-critical.
If we determine that it's in their best interest to support IE6, we don't line-item IE6 support (i.e. we don't say IE6 will cost you $xxxx extra.) We simply quote them a price that includes that cost (i.e. your website will cost $xxxx.)
If we determine that support IE6 will likely not matter, we break it out as an extra line-item cost and give them the option to support IE6 by paying extra. We explain the facts of their situation and let them make the decision.
It's not about making them feel bad. It's just human nature. It's just a more pleasant experience just paying a price and knowing it'll just work instead of having to pay more than the regular price just to make it work.
I see what you're saying, but it might still be useful for them to know what trade-offs are being made.
Like, "for this site and audience, we recommend supporting IE6. But FYI, that does eat this much of our costs, which can't be spent on shiny new features for modern browsers. So maybe for other projects, if you do something that targets a different audience, we'll want to make a different trade-off."
If I were the client, I think I'd appreciate that info. It might affect what types of sites I want to launch, for example.
If big companies are part of your core audience, they are part of your core audience. At that point IE 6 support is not optional, nor is pushing back on it going to make a difference. All you'll do is cause annoyance.
For some simple brochure sites, it's 4-6 hrs more of testing & tweaking during the lifecycle of the project, which usually translates to $500ish extra. i.e. 10-25% of the project.
For involved sites, it just depends what is being done and whether you're trying to replicate the experience or if you're just creating a graceful degradation for IE6 users, which is often "good enough" for a lot of clients.
For basic "looks the same" stuff this is probably true. The difficulty comes from clients who devise features that only work well on newer browsers, then insist on keeping the same functionality rather than "degrade gracefully" on IE6.