Ok, so let's say that they even want to block this trade, what's their reason going to be? Cos I'm yet to hear a good one...
And to answer your question, of course the AFL have a say in how the club is run but we're talking about one specific situation and no, I don't believe that the AFL tell the Suns who they can trade and who they can't. They would have a say in things that are much broader and much more important to the clubs sustainability than just one player, no matter how good he is. If they didn't like certain decisions that were made at the club they would simply just sack the people that are making those decisions so that they didn't have to worry about micro managing the hell out of the place.
So I'll state this again... If all 3 parties agree on a trade then the AFL can't and won't stand in the way of it. And in all honesty, GAJ potentially leaving the Suns with 1 year to go on his contract is the least of the AFL's problems when it comes to ensuring the long term sustainability of the Suns.