In the past I have done this using mulitple .git files. IIRC git searches up through parent directories for this file which can define the user, email and refer

In the past I have done this using mulitple .git files. IIRC git searches up through parent directories for this file which can define the user, email and referenced key file (well anything config wise) and you can then split the repositories with different parent directories. You can also avoid setting the global settings and do it for each repository which depending on how many you have might not be much of an issue.