I thought I was pretty much opposing your point. If you have to do more work for a client, charge them for it. It's like any piece of software development; agreeing the deployment platform(s) is a fundamental part of the technical planning stage. If I'm working on a mobile app, I need to know whether it's Android or iOS (or both), for embedded work I need to know the hardware platforms. For web development, the server architecture and browser/device support are pretty much top of the list. I always try to find out this information as early as possible, since IE6 support can sometimes be trivial if the design of the site isn't too outrageous and the client has indicated IE6 might be on the agenda. It's always an extra cost though; and is something I'll always make clear before any development takes place. As you no doubt know, it's far easier to work on templates and structure your CSS and markup if you know you need IE6 support, than it is to try to retrofit it later!
Some clients will be aware of the additional effort required, and make a decision, others require some explanation (I will generally suggest they check any existing stats if it's a rebuild, to see if it's worthwhile). It's hard to overstress how important it is to nail this down early; preferrably in a written contract that's signed off before development begins. It protects both you and the client, as you both know where you stand and there's no "oh, I thought it would work in IE6?!" confusion at the end that leads to a lot of wasted time, or aggravation. Usually at the developer's cost.
I've been quoting separately for IE6 for at least 5 years, and also IE7 for the last few. Of course, the additional cost is growing higher. Browsers have improved, while IE6 has not, and so the gap has in some ways widened. I'm finding that far less projects these days require IE6 support (of course, I do still check the sites are functional, but any styling issues are irrelevant.)
Do want to sound like I'm preaching, just been through it for so many years that this stuff is sort of automatic now!