I do agree with a lot of this article about the uselessness of enforcing outdated road rules to cyclists. I personally will rarely completely stop at stop sign. I find the danger much higher to try to immobilize the bike, un-clip the shoe and start again with a very slow speed (potentially exposing myself for a much longer period of time in that dangerous crossing zone).
To solve accidents between all of these actors, I think there should be a simple rule of giving the slowest vehicle always the right of way, which is what courteous people do. A pedestrians should always have priority over a cyclist and or a motorist. If accident happen, the cyclist/motorist should take the full responsibility for it. Likewise a cyclist should have priority over a motorist. The person at fault should be proven guilty unless proven innocent of some unpredictable situation.
It is a bit the same on the water, where motor boats have to give way to wind powered boat for the same logical reasons.