"All it takes is one bad experience during an auto update to lose trust in the system. With over half of WordPress installs tracked using 3.6 or earlier, we can ill afford to have anymore users disable automatic updates."

Yup. I do not use auto-updates for exactly this reason. WP needs to be gentle if it expects updating. Things like this break down should have incurred a warning: "You have plugins X, Y and Z which use bad practices which will be broken in an upcoming release" and then with the next release "You have plugins X, Y and Z which are not compatible with this release so should WP disable those plugins or abort the update process?"

No update should go around just breaking web sites. Bad, WP, bad.