Disqus has a blog post about how using there tool helps, http://blog.disqus.com/post/9956511178/disqus-research-how-comments-drive-traffic.
In the comments, Rob Webb asks the Disqus team about the SEO drawbacks of using Disqus because of the JavaScript not being seen by search spiders. The response from Disqus says that they aren't even sure if there are SEO drawbacks and that there are some ways around them, depending on the tool you use. Specifically, WordPress uses Disqus' data synchronization to resolve the SEO issue. The tool is something you could use to integrate Disqus.
I am not sure how difficult it would be to integrate Disqus with data sync but I do know creating your own commenting system is not simple. Here are the big concerns you need to be aware of if you write you own comment system:
- User Authentication - You need to use CAPTCHA or an authentication API (e.g. OAuth, OpenID) to weed out bots.
- Comment Review - You probably will need to review comments before they are posted due to concerns about bots getting around authentication or troll type users then you need to setup email and a allow/deny comment system. Even if you don't think you do now, that could change quickly after comments go live. For it to be easiest, the notification emails sent to admins should allow for them to respond to the email to allow/deny the comment.
- Comment Following - Some users like to follow comments by email or an RSS feed. That means you need a system that allow comment subscription that is thread specific and an RSS engine that will create RSS feeds for comment automatically for each page that gets added that uses Disqus.
- Hack proofing - Make sure users cannot enter any code into comment box that could hack or break your site.
All of these things can be done but they are not trivial and if you write the code yourself you run the risk of making the same mistakes that people have already made meaning there will be bugs and break-ins caused by your home grown comment system, that using something like Disqus will avoid.