There is currently no way to determine if someone has gone through step-up auth via the token. I did just add an issue: https://github.com/FusionAuth/fusionauth-issues/issues/1491 feel free to add comments there.
What you can do is use a JWT populate lambda to add a claim to the JWT if the user has any MFA methods enabled. When you do a step up you'll get a token and you can look at that claim.
HTH