There's a solution for that: use the LESS source. Mixin the various bootstrap classes into the styles you write for your clean, semantic markup. It's a nicer way to work, and it permits removal of almost all the presentational "bootstrap" classes from your markup. With some thoughtfully-structured markup, you can even do away with wrapper divs in many instances.
This isn't without some sharp edges—you have to grasp what the various moving pieces of bootstrap do, and what different mixins you must apply to achieve the desired effect, but it's a cleaner/more powerful approach IMO.
To be clear, I'm glad about the CSS-only approach too because it enables non-designers to get over the suck threshold quickly. Using the LESS is more work at first but it pays dividends in the long run.