We have already developed emulators that "programmed the bare metal" to test hardware before there was a suitable kernel available. It really wasn't noticably faster, and due to the fact that the power management driver was very simple (the driver in the linux kernel is a LOT more complicated), even when the emulator was sitting at a menu, it was eating up 100% CPU and drawing large amounts of power from the battery.
So throwing out Linux just isn't worth it, plus it would create a huge amount of inconsistency. For example, all of a sudden, you would have apps that ignore user settings, refused to sleep when the lid was closed, used up much more power than necessary, perhaps even caused physical damage (eg. If a certain pin on the processor is meant to be an input and is usually given an low signal, and your app drives it high, it would cause a conflict which could in turn cause the OMAP (or another hardware part) to overheat and malfunction).