^I wouldn't say "unwilling" exactly, not once they're inside the thing anyway. As I understand it the potential CPU is basically subject to a death of personality, a mindwipe that obliterates the person that was there and installs a new one. Indeed, this appears to be a necessary step and not a side effect of the process, hence the ship on Ganymede going nuts.
I must admit, as grisly a twist as this turned out to be, I still can't quite figure out *why* the Shadows designed their ships to require a living sapient to be grafted in as the CPU. It can't be raw processing power because machines can do that just as well, or better, nor can it be the inherent unpredictability (or "chaos", if you will) of organic neural linkages as that can just as easily be achieved through cloned tissues with gene modifications.
Perhaps it's a longevity thing? All those cycles of dormancy where they'd scatter their remaining ships on desolate worlds lead them to develop a system where the part most likely to degrade (the brain) to be easily swapped out for a fresh one. Perhaps if you did the same to a Vorlon ship, after a thousand years it simply might not work. The structure might be intact, the engines, weapons and power plant all of but the organic control systems are just inert goo. On the other hand perhaps the two technologies are fundamentally different.