I wanted to delete a marketplace asset from my project, of which I do know 100% that it has no dependencies outside of the folder it was imported. The editor report references still being in memory, and it kept reporting many reference errors on the deleting process until it eventually crashed. So I took a backup, and deleted the asset folder completely, without the editor running. The project booted up fine and compiled without any visible errors.
Now, is that safe to do? I would prefer not to have this method come back to bite eventually.
Well, you essentially reversed what the add content to project does (copy the MP folder to your project). As soon as you are sure about the nonexistent dependencies, you are good to go.
Also, run source control for every project, just in case 
If you don’t want that warning black cat, save and close your level and reopen it, it should now delete cleanly. If you still get that warning after this you’ll have to run a dependencies scan to make sure its definitely not referenced because chances are it is, somewhere and the tree will give you a clue.