I have an EFM32 board having Cortex M3. This board is having an Memory Protection Unit. Will it be a good idea to port Linux on it? I am discouraged because of this answer: Linux on ARM Cortex-M3 series, especially since I need a fast boot-up and efficiently running OS.
As others have alluded to in the comments of the question, I think what you are actually looking for is an MMU (Memory Management Unit) not an MPU (Memory Protection Unit). Among other things, a memory management unit is responsible for translating virtual memory addresses to physical memory addresses.
A memory protection unit really just keeps code executing in one mode (typically an unprivileged mode) from clobbering someone else's memory (usually the kernel's memory). This prevents a user program from bringing down the whole system.
If you are looking for a Unix-like operating system that you can run on hardware without an MMU (like Cortex-M based hardware), you might want to consider NuttX (http://nuttx.org/)