I've just re-read your original point, and note that your question closes with, "How can I specify different addresses spaces for the codes of the two programs?" (my emphasis)

This could be the root of your problem:
You no longer have two separate programs; you have just a single program, which is composed of an assembler part and a 'C' part.
If you really are trying to take 2 separate programs, and hoping that the Linker can somehow combine them, it won't work!
eg, if both the assembler and the 'C' are trying to set up the interrupt vectors, you're in trouble!