Yeah sadly. It doesn't follow any of the normal desktop Linux policies in that regard. I wonder if this can actually be fixed by nokie with an update sometime. It would certainly improve the ability to hack it around without breaking it(had it happen a few times).

Anything that is needed to boot the system to a point of mounting /usr should be directly in / not in /usr.

Maybe have a USR_OK event in upstart that would tell the rest of the scripts that USR is ok. It could be a dummy as a start but could be replaced by one that would mount it.