Method 1:
Use bench export-json and specify the DocTypes you want to export.
Reinstall the site (fresh with no data), install ERPNext in it.
Use bench import-doc with the path of the exported doctypes folder.
Method 2:
Comment out before_install hook inside ERPNext source code.
After installation make sure you manually create a Company, add fiscal year.
Tested using Frappe and ERPNext Version 15.