pyrohaz - Would you please tell us what it is you want to do? Then we might be able to help more effectively.
In theory, and depending on the board, you might be able to run the Beaglebone as a 'real-time' microcontroller, without Linux. However, there is likely a lot of work.
You'd need some way to load programs, so you'd need a JTAG adapter, and software like Open On-Chip debugger to drive it:
http://openocd.sourceforge.net/
I think the Beaglebone Black lost JTAG, but AFAIK the Beaglebone has it:
http://beagleboard.org/static/Docs/ccs-jtag-simple.htm
You'd need a cross-development tool. Maple's gcc might do the trick, or ARM's launchpad gcc
You'd need some libraries to drive the on-chip peripheral interfaces, It might be feasible to extract those from the Linux source, though they may be more complex than you need. So, trawl around for something withstand-alone (none-eabi) libraries
To do any of this, you'll likely have to overwrite the existing bootloader, so you might find it hard to go back to the original firmware.
This is all theoretical. So I have no real sense about how much work it will require. You might be able to 'brick' the board if you don't understand the details well enough.
It shouldn't be any harder than bringing up any raw MCU, and there may be some foks already working on one of the higher-performance Cortex-R or Cortex-M MCU's/SoCs.
An alterative approach is to look at the Open Source Real-Time OS sites (there are a bunch of them), and look for the highest performance board they support.
They must have a solution to compiling, loading programs, using the toolchain, etc. to get the RTOS to work on the bare metal.
They should also have start-up code and some libraries.
I'd start at FreeRTOS http://www.freertos.org/
though there are plenty of others. You're looking for a well documented way to compile, link and run code on 'bare metal', and peripheral libraries for the chip.
In the medium term (over the next year, or so) a good bet might be Parallella:
http://www.parallella.org/
It has a pair of ARM Cortex-M8 running at 800MHz, and a 16-core array processor.
I've seen benchmark graphs for the dual A8's (inside the Xilinx FPGA), comparing the real-time performance (jitter) for one core running Linux, against the other running a Real-Time OS. So I believe some work has been done by Xilinx or a partner.
