AtMega hangs up and doesn't respond to anything anymore
Do you mean the 32u4, the ar9331 or the Yun as a whole? What exactly stops happening?
Can you still ssh into the Yun? Can you still talk to the Yun over USB? Can you still access the Yun web interface?
I am quite sure that the issue is not a memory leak or a bug in my code;
Don't totally discount memory being the problem, the 32u4 has 2.5k of sram the Mega has 8k.
To see if the Yun is causing a RFI problem with your receiver, run your setup on the Mega and put the Yun as close as possible to where it would be if you were using it and power it up.