There are several reasons why we did not add an option for this. Actually, there was already an option for this (--embedded-video), but we simply decided to ignore its setting until the bug was fixed.
There are two problems here.
First, there would be no good default value. If we defaulted to embedded video, VLC would crash for a lot of users. And sorry, there is no way for the average user to figure out how to solve the crash. If we defaulted to non embedded video, we'd just about as many people whining as we've seen this far (and the Ubuntu bug reports have a lot more). And then we'd get distros and users recklessly enabling the option and shooting themselves in the foot. We don't like to let our downstreams and our users shoot themselves in the foot.
Second, if we had simply changed the default to disabling the embedded video in 0.9, people would be stuck without the embedded video as they would ugprade to 1.0, if they ever saved their settings. Not good.
I don't know for you, but I mostly watch videos in full screen mode. And even when I don't, I send most time watching the video, rather than play with the UI controls. This regression is very visible, but it's not quite as bad as VLC crashing pseudo-randomly, or sticking with 0.8.6. Besides, 0.8.6 also had the pseudo-random crash bug, except it was much better hidden than in 0.9. And you cannot blame the 0.9 series developpers for the horrible pile of race conditions that 0.8.6 was, thanks to not-so-careful former developpers.