I agree it sounds weird at first. On second thought, whether or not it is so strange depends on one means by "flight computers". For example, for something like logging or pre-flight checks the exact timing would matter that much, and it would be convenient to have a full blown OS. When timing matters (e.g. flight control?), I imagine that one could set up controllers (with their own CPUs and straight to the metal programming of the sort you described) as devices that accept commands from and stream data to the primary flight computer. This is %100 speculation. I would be curious to know what kind of temporal precision is needed for rocket control, since if it is a sloppy enough process then all this worrying about timing it for nought.