If we put the ideological issues aside there are some other potential issues about using Disqus that I have thought of:

1.) Control of data, I am not sure what rights I am legally signing away to Disqus when using it as my comment service.

2.) Continuity, I am certain that if Disqus passes away the service won't be there and only fools would offer a free service and ensure that the data isn't lost for what ever reason. How are your data liberation policies, a simple click for a zip or a tar-ball? Or would I need to construct my own back-up using your API? If the latter, is that allowed?