You can set-up a hostname filter in the admin section of GA. Best to do this in a separate view so that you can still access unfiltered data if you ever need to do so
The rationale for the discounts is that you don't know (or at least it's non-obvious), whether the discount is coming from the flight or the hotel. If the "Book together and save" amount is positive then you'll generally be getting a better deal than direct. You might see the same total price occasionally but it certainly won't be the case the majority of the time.