That darn spin.js error breaks things like the widget page, where you can't drop down the widget areas, for example.
We know about this issue. It's caused by a namespace conflict between Mootools' Spinner function, and Jetpack's own spinner. Although not that many people use Mootools in WordPress themes, RocketTheme does, and we would need to find a solution to solve this conflict.
Once reactivated, JetPack is automatically "connected" for all two dozen blogs on my network EXCEPT for the primary blog. Each time, I have to go into that primary blog and manually reconnect JetPack to WordPress.
Instead of deactivating the Jetpack plugin, you could try to activate a small plugin that would disable Jetpack's spinner function while you make your widget changes. You can use this plugin:
The code is available here:
https://gist.github.com/jeherve/5714915
You could also try to deactivate all Jetpack modules that do require the spinner:
Carousel, Custom CSS, Infinite Scroll, Notifications.
I hope this helps.