EDIT: found fix as described in this thread:
I am having this exact problem.
Installed FO3 GOTY from scratch (via steam)
Got the GFWL Disabler working
FOSE and Fallout 3 crash when run from MO, but run fine outside of MO.
Other executables run ok from MO like Loot and FalloutLauncher (but when i hit play from launcher, I crash)
I then modified the ini files as per Clear and Present Danger - didnt help.
Any help would be appreciated!
If the "fix" you linked to worked for you then I suggest you update your MO installation, that BSA issue has been rectified in later versions.