This is awesome, and I really appreciate the effort toward privacy/transparency. Along those lines, supporting do not track is great, but why use GA at all? Just implementation ease? Is this something you plan to move away from?
Well, GA is quite convenient - we get pretty graphs, realtime analytics and so on. It's not something we have considered moving away from, since it's trivial to disable it entirely. And it's not significantly worse than any other tracking tool.
That said, those all entail a lot of work and/or additional cost. You're also absolutely right that allowing users to disable it (and ads) is an amazing feature.
Piwik is really ancillary to the discussion at hand, but I often see the claim that Piwik can't handle busy sites, and it's important to quantify the claim.
I've had success (and others report similar behavior) with 500,000+ hits per day. http://piwik.org/docs/optimize/ reports adequate support to higher levels. It's quite easy to set this up with EC2 + RDS, and using autoscaling gets you a very resilient solution that can easy handle those numbers. Also, in the case of mediacru.sh, many of the optimizations have little impact since they optimize for reporting on the already-gathered analytics. With only two analytics viewers/users - this is not much of an issue.
If you're doing more than 1mil per day, then I think something like snowplow, a commercial solution, or a fully custom solution are appropriate anyway.
There is no excuse for not running your own: http://demo.piwik.org/
Also worth reading: http://manurevah.com/blah/en/blog/Like-this-if-You-are-Again...
We've realised that self-hosting our analytics might be a better choice. I've created an issue[1] to discuss this matter. Ideally what we'd want is something as close to GA as possible - real time analytics being reasonably important.
Note: we were aware of the implications of using GA on the site, but since we offer the ability to disable them very easily we didn't think it was a big deal. That's a mistake on our part, so let's discuss how to fix it.