My idea is that before an autoupdate is executed that a few checks happen. This could reduce the probability of a website going offline.
If there is high probability that the AutoUpdate will complete successfully then it proceeds if not then an email is sent to the administrator with a warning.
To do this can be complex however by utilizing wp.org I believe it can be automated to a point where reliability is improved.
The method would be...
Have AutoUpdate look for installed plugins and themes.
If the authors have already tested and 100% compatibility has been stated by a plugin author or theme author that item passes.
If users are marking a plugin as Broke for a specific version of wordpress then that is taken into account.
If a third party theme or plugin that is unknown as in commercial ware is being used then that item is marked as a .. Maybe or Fail.
It may also be possible to test core themes and plugins or ones distributed by wp.org for a CRC test of the files.
This can be easy to difficult to accomplish however with users in the ballance it seems reasonable to work on such a method of checking version numbers, plugins, themes and maybe a CRC check then defining a level of probability that a AutoUpdate will execute without problem.
More so this test would not look for Maybe plugins and themes...
It would look for the use of any plugin or theme that is KNOWN to fail an autoupdate and then halt the update process with an email to the admin to make changes.
Additionally when a core function is deprecated or something else that is as drastic is in the new update such as PHP dependency or other it could be possible to scan the theme and plugin repository for use of those methods in the latest version of those items and then halt an autoupdate if that feature is being used by the website in question.
sorry a little wordy..
but i believe this is a good direction
especially the use of the wp.org repository data against any update.
if the data is available and not used and that leads to an offline website especially a commercial one no matter if its a 1 person company or a fortune 50 then it is responsible coding to use that data and not force updates...
Because a dead site is a dead site no matter if its by user error or automation.
it makes people sad.. and you lose A LOT OF GOOD WILL if one person spreads the word.
Believe me that is the first thing that all large corporations tell every new employee.
Many customers will never spread a good word about something .. but for every single person that has a problem they will tell dozens of people.
This is why Angies List can charge people to complain about companies and products.. people will even PAY MONEY to complain...
So its very important to use resources correctly and treat every good willed person with respect rather than discount them as not worthy of attention when they are helping you.