This bug is created as a clone of upstream ticket:
https://fedorahosted.org/sssd/ticket/2335

We need logic in SSSD that would allow the GDM prompter to prompt the user for long-term password and the OTP in different prompts. 

Nathaniel suggested to use the krb5 responder callback. Citing from his proposal:

That is, the user name is selected in GDM and SSSD begins the krb5 connection. The responder callback is called. Within this callback, SSSD can see exactly what mechanisms can be used to authenticate the user. No connection to LDAP is needed. This should drive the responses (all within the callback). There is no guarantee that SSSD’s analysis of LDAP will drive the choices actually available in the responder callback.

However, I don’t know how this could be done while preserving the communication protocol between the parent and child processes.