Sure you can! Here's how I do it.
1.) Make sure you have no duplicate systems.
2.) Create a new folder in the system tree and call it dupes.
3.) Import your list of systems to be deleted into the dupes folder.
4.) run the duplicate system query and delete BOTH systems.
5.) revisit the dupes folder. Any systems remaining in there did NOT match a system currently in ePO and can be deleted.
Hope this helps.