Where are you getting the different rate from? Most car rental companies I have dealt with have rates per 24 hour period and returning early on the same day isn't penalized. If you return on a different day the rate structure could be different (weekly rate vs. 6 days), so if your 7th day (24 hour day) doesn't start until 10 AM in the morning on the day you return you will be charged 6x the daily rate (which is probably more than the weekly rate) to return at 6:30 AM. There are also weekend rates and if you don't meet the minimum number of 24 hour days for that (by returning too early) you will not qualify for the cheaper rate.
Another thing to check is that the car rental company has hours of operation (or a night drop off) at the time you want to return (could be a problem at smaller airports that don't stay open 24 hours/day).
If this really is happening due to a policy and not a mistake you can probably find some corporate rate code or other rate code to book with (maybe
AAA or Costco) that allows for an anytime return.
Have you tried checking prices on Hotwire? There are no refunds or changes once booked through Hotwire so your dates have to be firm but many times I find better prices on Hotwire than booking direct though the car rental companies.