After dying, Programs don't go to Limbo, they're return to The Source (the Machine Mainframe) to be judged. If they're found to continue to be useful, they're returned to the Matrix. If not, their code is recycled.
Given that the Keymaker is an essential component of the Path of the One (leading from the Oracle to The Keymaker to The Architect to The Choice) it's highly likely that under normal circumstances if he's killed he'd just be given another shell and decanted back into the Matrix to do whatever it is that he does when he's not guiding The One. It's not clear whether this particular Keymaker has survived multiple reboots, nor is it especially relevant. If he dies, he'll just come back again.
Unfortunately, with the end of The War and the breaking of the Path of the One, the Keymaker appears to no longer serve a purpose. It's likely that his program would be terminated.