Do we need an individual JS file from VGS for every site using Secure Form?

No. We can create a single JS file for all your sites. For example:

SecureForm.create('site-1', ...) // this form will submit to site 1
SecureForm.create('sandbox-1', ...) // this form will submit to sandbox-1
SecureForm.create('live', ...) // this form will submit to live