It is possible for any subsystem to "crush" and ruin the rest of the setup. However, the safeguide you have only work well if you are monitoring it all the time. As soon as disaster strike, you only have a few hours to shut off the refug. which is very rarely possible if you need to work or study.
However, it does not means that it is useless. Maybe it will comes in handy when you happened to foretell the problem. Althought I doubt that most people will be able to take advantage of it, it does not mean that there is any specific reason to not implement it the way you wanted. Keep in mind that you still can move the skimmer before the pump, but with high recirculation rate, it should not make much difference in skimmer efficiency.
One thing that I would like to add is that you may want to add a "Y" to the left overflow, the one that drains into the refug. This is because you will be able to adjust the amount of flow going into the refug. and let the excess drains into the rest of the sump, just like the other overflow. This way, if one of you overflow is blocked, you still have the other one to handle some of the flow without flushing out the refug. Complication will be overflow noise, but you don't know until you get it setup.