Using multi-factor authentication is one of the easiest and most effective ways to increase the security of your organization. In summary, to provide an additional level of security for sign-ins, you must use multi-factor authentication (MFA)
And to my knowledge, you won't have to do the second step every time you sign in. Some people worry that multi-factor authentication is going to be really inconvenient, but generally it's only used the first time you sign into an app or device, or the first time you sign in after changing your password.
So as @collinq said, it is suggested to disable it and use a Service account whose MFA is disabled instead if you want to configure scheduled refresh.