Here are some instructions on how to disable matrix at boot time: http://processors.wiki.ti.com/index.php/Matrix_Users_Guide#Matrix_Startup_Debug
I'm not sure why it would say that matrix-gui-2.0 doesn't exist. Did you trying cd'ing into that directory and checking if it was there?
In the dual camera source code, all of the manipulation of raw camera data occurs in loopback.cpp. There is a function called "display_frame" where the raw YUV data is taken from the camera capture buffers and placed into the framebuffer for display; you could copy the camera frames to any buffer, though, if you wanted to do processing on them. Note that "display frame" uses double buffering to eliminate tearing, so there are 2 different copies that can occur depending on which buffer is being used.