They might take issue with a couple of things like https://issues.asterisk.org/view_license_agreement.php , "commercial edition" based on the open one, deals between asterisk and skype which makes closed-source skype channels available for asterisk (who knows how would it affect skype-competitor plugins) and many others. While nothing critical, I think GNU people might not entirely like it.

The fsf/GNU isn't anti-commercial, just anti-proprietary. Free speech vs. Free beer. I doubt Asterisk dealings with Skype for special access for it's customers that pay a preium service fee really bothers them, except maybe helping Skype propagate it's proprietary tech indirectly.

What asterisk does is no different than MySQL and QT.

Here is a debate where RMS talks about the dual license issue. http://www.youtube.com/watch?v=lrVayqOHbZw He basically says it's acceptable.