Can this RAM bypass be prevented by making the particular memory controller "not idle"?
That patent doesn't do what he thinks it does.  The patent is a method for changing the components of a memory controller during design so that you can support a collaborative bypass of the controller within the various components or stages of the memory controller itself.  No where do they describe sitting on the external memory bus (to DRAM) and snooping on it.  In fact they describe a controller that says "hey guys - I'm idle now, go and do your stuff"

When they say "components" think " functional blocks" not DRAM modules or the like.