Did Carlos Boozer get a fat paycheck? Of course he did. Many GM's pay for guys who can fill up the statsheet. Plus, Kanter's weaknesses would not be so evident if he wasn't playing on such a terrible team. He's a slow defender, but his guards, especially Burke, are really terrible at defense also, so he's constantly having to make decisions on where to go and how much to help, etc.., which is the last thing you want him having to do.
But point is, GM's are definitely going to overlook his defense because bigs who can score at the rate he's capable of are a prime commodity. I'm not saying they should it, simply that they will do it.