Honestly, I don't think Rory fukk with Mal like that. Mal is a loner type nikka who dap a lot of people up, but don't have hardly any close friends.
Rory exposed how he felt the first episode when he said Joe was right about the books, and they
were overpaid. Rory didn't care that he was disciplined by Joe and even agreed with Joe that he was a little off the handle those last episodes before he was told to stay home and cool off for a few days. You have to remember, Rory was/is a diehard fan of Joe from a music standpoint.
Mal was the one who turned into Al Sharpton and blew the spot. So Rory had no choice but to go along with it to stay in the game. No doubt in my mind if Rory had his way he would be back podding with Joe with Mal gone. He just don't want to seem disloyal.