I think your point is easily solved with a capital gains deduction or marginal rate, where the first X of annual (or averaged annual) gains are exempted. So a person selling $50,000 (or whatever) or more would see a higher rate, thus people withdrawing from their retirement account wouldn't be hit by an increase.

The main reason I would increase the capital gains rate is the very richest, like Warren Buffet (as he himself pointed out), pay a lower rate than much less wealthy/lower income people due to the favorable capital gains rate. This sort of inversion shouldn't exist in a progressive tax system. Personally I view one of the several valid goals of a tax system to be keeping income/wealth inequality within reasonable limits and I think this would help with that.