The minimum order value feature applies to the whole site, as you mentioned. It cannot be applied to parts of a site.
It's possible to write code that can emulate the built-in minimum order value feature. A number of guides and videos were produced in the past that explained how to do this. However, a custom code solution will only help upto and including the cart page. When customers reach the checkout page, they will be able to remove items and checkout with a lower than minimum order.