Indeed, I think the BSG analogy is a good sci-fi warning about the outcomes of moving away from heterogenous systems.

Environments engineered with multiple failsafes, defense in depth, avoidance of SPOFs (including hardware models, manufacturers, chipsets, OSes, web servers, etc.) will be very difficult to fully penetrate and should be able to survive attacks.

Of course none of the above is cheap or fast to do, so it usually doesn't get done.