You can very well delete a site in alfresco share. However, what happens to the workflows in progress in the site?
If you delete a site, the workflows remains as it is. For example, if you have document approval flow going on in a particular site, and then you delete the site - the workflow still stays, thus when you try to approve or reject the document, it behaves erratically.
The workflows should also be cancelled or deleted while you remove a site in alfresco.
Same applies to any space as well? It should first check if any workflow in going on in that space or sub-space.