Not sure I 100% get the problem, but see if this doen't help:
- Remove code from email to support case script that sets field "customForm".
- Create specific role for user used to create the cases - don't assign a generic role, like "administrator".
- In code for script, specify the role you created in #2 for the login/authentication.
- Now, you can flip back and forth between forms from the NetSuite UI by making the needed form the default for the role you created in #2.
All other users will be unaffected, and you won't have to modify the script going forward, except if you have new functionality to add to it.
The other option is to always make the script use the standard case form. That way, you'll never really need to change it. The standard form will contain all custom fields and all standard fields. The only thing you would then need to control is the preferred form by role.