Silently adding Guest users to Azure AD

Not tested but You can programmatically create guest users using Invitation API and save the the redemption url generated against each guest user name probably in a csv file. Later on you can send email to each guest user with redemption link. In Azure AD, you can configure conditional access (MFA) since start for usertype = guest. When guest user will receive your invitation email and try to redeem the invitation, MFA setup will automatically trigger for the user.