I guess that the issue I take with using the CogAT in lieu of IQ is that it isn't a controlled test. Parents can pose as homeschoolers and get the test from a homeschooling organization, teach their kids the answers, and use those scores. We know at least one family that prepared their child in a manner of this sort to get into GT programming in school. Of course, anyone who is willing to do something of this sort probably doesn't have his/her kid's best interests at heart.
I probably also have a personal bias in that dd#2 who came at clearly gifted on the WISC (although with scores at the 99.9th and 97th on two different administrations of that test, so erratic), was just above that 1 SD point on the CogAT. That probably makes me less than fond of that test as it was used by dd's teacher to discount her IQ scores.
I would think that someone in your shoes who prepped for the CogAT was acting in their child's best interest. Sometimes you can change 'city hall' and sometimes you can't. I agree that the system stinks.
