I agree with bogdacutu, basically you need to be able to read the memory space of the memory card.
Like an HD does not need to be formatted in order to be able to read sectors of of it.
The boot loader basically acts like the Bios of a pc. Only here you can not specify where to look for
the 'application' that needs to executed. That location is hardcoded into the boot loader.
So you are left with few options:
a) A hardware solution to what is basically a software issue, kinda overkill I feel.
b) A modified boot loader (not for the faint hearted), basically change the start location.
c) A program on the MMC that loads the app from the MC (Kinda like a boot loader on pc where you select the OS you want to start).
Unless the compiler is more powerful and feature rich than documented it looks assembly your only option.
Write the loader program in assembler, this allows you to use the full potential of the MMC (you'd need the instruction data sheet)
and bypass the 'higher language' and subsequent compiler limitations.
Either way the path is steep.