As @lokesh mentioned, OOB you cannot restrict the workflows based on the sites.
As a solution you can override /libs/cq/ui/widgets/source/widgets/wcm/Sidekick.js file and customized the list according to the sites you have.
Workflow list using the below service /libs/cq/workflow/content/console/workflows.json?tags=wcm
Create your own service and customize the JS to use your custom service that would work for you