The GNU HC11 simulator contains a simulator for the builtin eeprom chip. You can disable the eeprom by specifying --cpu-config=0xe option.
The --cpu-config=N allows to set the value of the 68HC11 config register.
(So specifying it is equivalent to programming CONFIG and restarting the CPU.) For bits definition refer to the 68HC11 manual.
To use this option:
m6811-elf-run --cpu-config=0xe (gdb) target sim --cpu-config=0xe