Working with less technically inclined folks, especially family, is a real challenge and working out when and how to compromise is a constantly evolving skill.
It sounds like your wife is using your 1Password account despite having a Family plan. It seems likely that she is using your account(s) on your device(s), too. She needs to have her own 1Password account as a member of the Family and her own account on any shared devices. She will have her own Private vault in addition to any vaults shared with you.
This will involve work, most of which you'll need to do, with her co-operation. The benefit for her is that she will end up with everything set up for her needs and preferences, with you able to guide and support her.
PS. Your mention of passkeys in the title suggests that I may have completely misunderstood your question despite re-reading it several times, though in that case I plan to blame you.