What is done currently is that there is a number of average civs. That means that there are 30 civs, but only a capped number is alive at a single point of time. The others are collapsed.
In this case you already have kinda of the proposed feature but without any unnecessary randomness.
Randomness would actually spoil the gameplay of RFC. See, all civs are interlinked with each other. Like when Spain is supposed to conquer the Incas it would be kinda stupid if there are no Inca.
Also several civs have the function to balance each other. This is especially true for Europe. So France and Russia are balancing Germany. If there is no France then Germany would be a Super Germany, which would spoil gameplay rapidly. What I mean to say is that all civs are balanced in a very subtle way but nevertheless complex way.
A few examples :
Russia has no enemy to the east, therefore Siberia is a REALLY crappy place. (this is done by marches, tundra, less ressources etc.) India has a whole subcontinent alone, but is not suppose to rise before very late in the game, therefore there are lots of jungles in India etc etc. Not the mention the endless deserts and mountains in the 'natural' Mongolian territory.
European territory on the other hand is boosted excessively, because it has to host historically high rising Civs on minimal territory.
Therefore if suddenly a few European Civs are missing then there is a real problem. In this case there would emerge an ever dominating European Super Civ.