Hello Amit,
There are ways to remove usage types but you would probably fall foul of "unsupported" unless it's done by SAP hands.
I would open a message with SAP and ask them the way forward explaining you want to do a DSS on a system where a usage type (PI/MI) was inadvertently installed but has never been and is not used.
The suggestion to perform a system copy does not resolve your problem as even with the copy method the usage types would still be there and it would be unnecessarily complex.
Kind Regards,
Amerjit