Given that the LM could land itself without an astronaut piloting it, did it have other mechanisms in place to override any extreme commands that would have crashed the ship?
No, there was only very elementary automation. The control software was only a few kB of code (about 4kB), not enough to fly the module safely even without a pilot trying to cause harm. Neil Armstrong famously had to change the landing site and land manually as the module was about to land in a rock field.