Like atani suggested I also use Keybindings, you have to set a key to remove atoms, like Delete, save that as a profile and then you can just hit delete and the selected atom will get deleted.
If you have lots of atoms, a faster way to do mass operations in scenes is to edit the scene .json file directly. If you do that you might want to use notepad++ and set the language to JSON so that you see where the accolades beging and end. Basically each atom is a block like { "id" : "AtomName", ....other stuff}. You can just search them by the id, go to the accolade where it starts and delete that whole block and save the json.