Dom,
No problem hooking them up as you described.
Plug one of them into the battery port in the receiver, and plug the other into an empty channel, or into a "Y" harness.
I believe that RED's Battery Clinic, (which I don't have the link to), explains the old wives tale about one batterty charging another. Perhaps someone else here has that link and can supply it to you. If both batteries are the same or are close to the same capacity, no sweat.
The person that told you about the problems should do the same reading too.
RED's battery clinic might be accessable from Fromco's website too.

I have flown two battery packs hooked up like this for years, and never had a problem. I'm sure that many others have as well, and could relate their experiences to you.

Check out the good information on battery packs at www.hangtimehobbies.com. No BS batteries is a very reliable and good source for battery packs.
I trust all of my BVM Jets to their batteries.

I'm using their 2400 CP-2400SCR 6 volt batteries....redundantly.

Here it is! www.rcbatteryclinic.com hit the button for "paralell battery packs" (on the left side) for the full story.

Harley Condra
BVM REP
JetCat REP