Does un-checking the "cleared for sale" checkbox do this? I am afraid to uncheck it. The language that appears there is ambiguous. It says, "If your in-app purchase is currently available for purchase, it will be removed from sale on the App Store". Does this mean my entire app will be removed from sale or just the IAP?
Yes, do that for the IAP products. That process won't affect the app itself.*
An option to delete, if that's your end game, should appear after a product is taken off sale (cleared for sale 'no').
You may know, but be sure you've disabled IAP as an app capability via Xcode as well. Requires update to that project/app in the store.
*Deselecting all countries (rights/pricing) will take the app itself off sale from the store.