How to add a "Remove Taxonomy term" option to VBO instead of only "Add taxonomy term"?
You could try to perform a bulk operation using logic expressed in a Rules Component. More details below ...

VBO comes, out of the box, with some predefined (hardcoded) operations that is to be applied to each row selected in the view. The available operations are shown within "Selected bulk operations" when configuring the VBO field. In your case "Add the selected terms" seems to be one of those. While something like "Remove the selected terms" (as per your question) is not included.

However using Rules (Conditions and/or Actions) you might probably get it to work, i.e. by execute a VBO operation which you define using a Rules Component. To get the idea, have a look at the video about Using Rules components with VBO" uses a Rules Component with (only) 1 parameter. If you want even more, then also watch the subsequent "Using Rules components with more than one parameter" video. This video actually shows how to (also) add a term to a node, so it should be pretty forward to use a similar technique, and perform a remove instead of an add of a term.

Note: to process 100.000 nodes at once is quite a challenge (memory requirements, etc). Therefor you might want to also watch the video about "More details about VBO settings" ... Before you are tempted to use VBO for processing them all at once ...

Happy VBO-ing while Rules-ing!