I think that without setting "treat JPEG files next to raw files as separate photos" LR effectively ignores the jpeg. When you go to a folder in LR, it will tell you if it sees jpegs (by the "raw+jpeg" message), but I think they're not actually in the catalog.
If that's right, you can probably just delete the jpegs (in Windows Explorer or Mac Finder) and LR won't mind.
However, just as a check, I'd try deleting one or two, see what LR does, and if all hell breaks loose then you can always restore them.