I finally figured out a way to replace hard-coded links to site feed URLs to their respective FeedBurner URLs in the site's source HTML. This option can be enabled in admin/settings/feedburner under the 'General settings' section. Since this is kind-of experimental right now, please test it out and let me know if there are any problems.

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Status: Fixed » Closed (fixed)

Automatically closed -- issue fixed for two weeks with no activity.