If you're worried about "owning" the data/community, you could host your own discourse (http://www.discourse.org/) instance and use their embed feature (http://eviltrout.com/2014/01/22/embedding-discourse.html).
Embedding is sadly missing inline commenting, though.
On the other hand if you are just working on MVP, and comments are not your main value prop, and you just don't want to bother with implementing your own system - sure, whatever, go for it. There's nothing too horrible about disqus, it's fine.
+ Highly customizable
+ Loads of moderation options(whitelists, blacklists)
+ Active community
+ Easy to use admin tools
- Seems to load slowly sometimes
Also, the most compelling reason for using it is that you don't need to waste time coding your own commenting system. In the future if you decide to make a commenting system of your own, you can always export comments from disqus.
But if the comments are just an add-on with little SEO value, then sure, quick and easy.
I don't like enabling semi-arbitrary JS from one place among all the sites I visit.