Hey Disqus-- what if you released a Wordpress plugin version of Disqus that used, say, web services to pull the content from disqus and serve it directly from the blog host? Solves the SEO problem and the JS problem.
For the "data security" problem, you could store a local copy of all the comments at the blog hosts, and a migration tool to port them back to wordpress native comments if someone leaves the service.
We actually already do that with our API version of the plugin. We're currently working on a new plugin which should deprecate our old JavaScript version.
I think it would be best to provide a standard solution that works for most users. The other chunk (people like you/me) can develop on top of the API creating whatever custom solution we need.
This is a win/win.
The other problem I see is being able to customize the comments.
I haven't played with Disqus enough to know this--but being able to customize the comments (IE: Strip out CSS and customize with my own, re-organize using my own markup, strip JS if I choose to) may be an issue for me.
Disqus looks the same across every blog I visit. Adding a way to customize comments would be extremely helpful.
As joshwa said, both of these problems could be solved with a better integrated WordPress plugin. Not to mention it could easily be extended with a more developed API.
The good news is Disqus seems to be listening. I see them replying everywhere they're talking about--which is great.
These are the primary reasons holding me back from using Disqus, any thoughts on adding these Disqus?
Did you prefix your comment with "@Joshwa" as a clever way of pointing out that some people don't care if the comments are threaded, when the comment count is low?
For the "data security" problem, you could store a local copy of all the comments at the blog hosts, and a migration tool to port them back to wordpress native comments if someone leaves the service.