It has nothing at all do with paying a second fee. It's about bandwidth. There is very limited space on the WA. I can assure you, people want their RSN's in HD before any of the channels you listed, and probably more than Disney in HD. There is room on the EA, but even there if RSN's went full time HD it will start to fill up unless they start to make more use of 77. No one is clammering for the channels you listed to be in HD. That's why.
Your other assumption is also wrong. The free HD for life, is a business gimmick. If you go with the two year commitment, you will most likely stay for the two years to avoid the fee. If you pay the $99, you will also stay for awhile to get your money's worth. The opposite of what you are trying to say is true. It costs dish to carry everything in HD, in that it is causing them to add satellites, and spend time moving channels around to fit everything, and to use new technology. (MPEG4) They are also faced with getting the WA to MPEG4, and get everyone with the old receivers into new ones. All costs big money. So if anything the two year commitment or the $99 goes towards their cost to provide them, not because they are paying more for them.
Why would you think they are picking on Disney, to not pay a second fee to, and pay someone else a second fee? And how would they have won their lawsuit? If they were paying everyone a second time, your bill would go up far more than it does. This is all Disney. You can be sure, as a poster above pointed out, Dish would simply get the HD feed, and drop the SD one, but most likely Disney will not allow it. Dish is not about to set a precedence and pay Disney twice.
whatchel1 said it quite simply and effectively above.