Yes, it is possible to make a site inactive in our ServiceDesk Plus-MSP portal.
1. The site which you want to mark as inactive should be used atleast by any one module. (example, it should be associated to one request)
2. Now go to Site list view screen, select the sites that you want to make it as inactive -> go to actions -> Delete site.
3. You will get a pop up message that site cannot be deleted as it is being used by a module. (refer the screenshot below)
Thus closing the pop up message, the site will get grayed out from the site list and will become inactive. (refer the screenshot below).