I have the same problem on my site. For example, my RSS feed at https://www.rfc1149.net/blog/feed/rss2/ contains:
<description>
I see more and more sites containing ads provided by [Google][] through its [AdSense][] program. Out of curiosity, I went and check their [Online Terms and Conditions][terms] and was stunned by the requirements set out by [Google][].
In no event, however, shall Google make payments for any earned balance less ...
</description>
Only the description and the trackback text seem to be problematic. I have the following in Markdown 1.0.1:
# Add Markdown filter with priority 6 (same as Textile).
add_filter('the_content', 'Markdown', 6);
add_filter('the_content_rss', 'Markdown', 6);
add_filter('the_excerpt', 'Markdown', 6);
add_filter('the_excerpt_rss', 'Markdown', 6);
add_filter('the_excerpt_rss', 'strip_tags', 100);
add_filter('comment_text', 'Markdown', 6);
