EAGLE restrict area isolation
First of all, my internet is off and I'm on my mobile, so I can't post screen shots. I'll do that later and go in in more detail. 

You are right, it's due to the isolation, and net classes would be a solution. Typically, you would like to have more isolation for high voltage signals, or thicker tracks for high current signals, while all other signals can follow the standard design rules. And that's exactly what net classes are for. 

In your case, create a new net class with isolation 0, and assign the signal GND to this class. Now, there will be no more space between your rectangle and the polygon, while the polygon respects the isolation of all other signals being in other net classes.