They are prohibited from selling handgun ammunition to anyone under the age of 21 by 18 USC & 922(b)(1). It has nothing to do with store policy at all, or even state law. It's a Federal Law and has been for many, many years.
Here is a partial quote: Federal law prohibits Federal Firearms licensees from selling or delivering "....any firearm or ammunition to any individual who the licensee knows or has reasonable cause to believe is less than eighteen years of age, and if the firearm is other than a shotgun or rifle, or ammunition for a shotgun or rifle, to any individual who the licensee knows or has reasonable cause to believe is less than twenty-one years of age."
"Ammunition interchangeable between rifles and handguns (such as .22 caliber rimfire) may be sold to an individual 18 years of age or older, but less than 21, if the licensee is satisfied that the ammunition is being acquired for use in a rifle."
These quotes are from BATF&E's STATE LAWS AND PUBLISHED ORDINANCES-FIREARMS, 25th Edition.
It's obvious that the clerk and manager were choosing to err on the side of caution, since there aren't that many .45 caliber rifles. There are a few that I can think of, but the average person wouldn't be aware of them.
My suggestion is for you to go alone and buy the ammunition and give it to your brother, which is perfectly legal, since it's going to be used in a rifle. It wouldn't be prudent to take the rifle inside a Wal-Mart store to prove it's existance, so this would be the easy way to circumvent their store policy. You can't really blame them for trying to protect their license, and if they really don't know, then they took the proper action in this case.
Hope this helps.
Fred