Yes. Use the MFA Exemption permission rather than disabling MFA for your entire organization.

To set this up, create a copy of the user's current role, add the MFA Exemption permission to that new role, and then assign the exempted user(s) to it. Everyone else keeps MFA as normal.

Keep in mind that enabling MFA doesn't force a user to complete setup right away - it simply shows a banner and prompts them to configure a second factor at login until they do.