Disable multisite for external website that uses wordpress header/footer/theme

Hi people.

i have a particular situation with multisite :

i have multisite enabled at domain.com with subfolders.

and i have one subdomain at subdomain.domain.com, which is actually NOT wordpress but an external script.

but that script is wrapped in wordpress template header/footer from domain.com

the problem is, even when i include rules to htaccess to not rewrite that subfolder (the subfolder named ‘subdomain’ in this case), and if i add that particular subdomain name as banned word into multisite options to prevent sites from being created with it, wordpress redirects subdomain.domain.com to domain.com

what i want is ;

subdomain.domain.com which resides in a REAL folder named ‘subdomain’ to be able to include wordpress theme’s header/footer, and therefore be wrapped in wordpress theme.

can you give any pointers for that ? ty.