Tyler, this is from our email correspondence, but I don't want it to get lost. I had a lot of trouble due to this issue, so I would like to see it fixed in the code.
Some WXR exports which I believe Disqus uses to sync existing comments back to Disqus are broken and don't validate due to incorrectly escaped CDATA tags (that is, if your post content contains CDATA tags). For example, we have a few posts with Rafflecopter widgets (for giveaways), and those widgets have CDATA tags already, which breaks the WXR.
See http://core.trac.wordpress.org/ticket/15203. It's fixed in the next revision of WP (3.4), but right now XML isn't valid.
So, I took the fix from there and applied it manually in my WP's core export.php - it's just a 1 line change (http://core.trac.wordpress.org/changeset/19858). Check this out - the 284MB dump validated after this! So this fix is absolutely necessary for everything to parse.
I then looked at your code and found that rather than using core export functions, the Disqus plugin uses a modified copy, made from WP 2.8. Specifically, the patch needs to be applied to dsq_export_wxr_cdata() - otherwise the patch made to WP won't have any effect.
I don't know why you guys are copying core functions straight up like that, but it opens you up to bugs if you don't follow commits to the same functionality in the core. I'm not sure whether the team followed updates since 2.8. I'm going to make this change on my end manually, but this should be committed to the plugin.
It's worth noting that at the top of export.php in Disqus, we have
define('WXR_VERSION', '1.0'); while the core one is now at 1.2.