Thanks for the feedback!
The article you linked to brings up interesting questions. Matt tried to answer all of them in the comments there.
If, however, you find conflicts between Jetpack and your theme or one of your plugins, do not hesitate to post in the support forums, or contact us via email. We'll be happy to have a look and see what we can do.
But the real problem is that JetPack is intrusive: it takes over entirely too much of my WordPress installation.
If you're not interested in one of the features included in jetpack, you can always deactivate the module in the Jetpack menu.
We're continuously working on improving each Jetpack module, but if you have feedback about one of them in particular, let me know!