Not sure I totally see the problem. Are you concerned that a user could claim you used their private key because you have access to all users keys?

Private keys should ideally be stored one for each user and not in the system itself. I don't know the ins and outs of your system, but could you not get each operation to require the user to attach their private key to complete the operation (this could even by handled client side in some sitations so you can maintain a true 'Trust No One' approach)

If you are concerned users will claim they never owned the private key can't you make a step in the operations to require proof of private key. Such as requiring the users to decrypt something you system encrypts using the public keys?

Not sure I totally see the problem. Are you concerned that a user could claim you used their private key because you have access to all users keys?

Private keys should ideally be stored one for each user and not in the system itself. I don't know the ins and outs of your system, but could you not get each operation to require the user to attach their private key to complete the operation (this could even by handled client side in some sitations so you can maintain a true 'Trust No One' approach)

If you are concerned users will claim they never owned the private key can't you make a step in the operations to require proof of private key. Such as requiring the users to decrypt something your system encrypts using the public keys?