How about a “Temporarily Disable Tool” feature where the tool is disabled? Just the same as the "Disable All Tools that Write Output" but would only apply to the specific tool you select. But, Instead of having to delete or cut the tool and connect around (as this can be tedious)! The feature could be applied to various preparation tools (and potentially more) to help save time.
For example, there are occasions when I might have a filter applied and would want to temporarily disable the tool only to see all results. This has been the case when I have wanted to include hospital wards (by temporarily disabling the tool) I was filtering out to review in the summarized totals.
The specific tool could have the same hashed marking as the "Disable All Tools that Write Output". The "Temporarily Disable Tool" feature could be listed when the specific tool is right clicked on. - The workflow could also prompt to show that the user has a tool "disabled" to highlight to the user.