The User record in each org for each user is independent and has a Profile defined on it directly.
If you have a user who is known in the IdP store as:
email@example.com, the configuration of the two orgs' User records for Joe might be configured like this:
Org 1 - Sales
Org: Acme Sales
Profile: System Administrator
Org 2 - Service
Org: Acme Service
Profile: Helpdesk Supervisor
The one consideration which you'll need to address comes into play with the just-in-time provisioning of users into an org if they don't exist there yet. The just-in-time provisioning SAML response will typically include the Profile which the user should have when they're created.
In the example above, if the SAML response for just-in-time provisioning indicated that Joe should be a System Administrator, and that was sent to the Service org - Joe's user record will be updated and his profile will/can be modified from Helpdesk Supervisor to System Administrator.