There was a recent commit that made the checkout process table-less in the Commerce Issue Que. It was reverted in favor of making such a large change to the codebase on a 2.x release. That code still exists and it's all possible using theme_ functions in your template.php...
/modules/checkout/includes/commerce_checkout.pages.incand look for functions that start with theme_
Let us know in the comments if this process worked for you! Also, post any tweaks to the Commerce Issue Que and they might be considered for inclusion for the 2.x release.
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