Where did this even come from? Joe's Passenger has shown no signs of ever being anything other than being on Joe's side. Is it true that Joe's Passenger is biased in regards with his information? No doubt about it, we have plenty of WoG on it. Has it been shown to be in some degree amoral? Definitely, hence why Joe was so horrified at how blase it was to Aisha's past while also playing favorites when it came to the Undersiders. And can it be difficult to understand? Of course, regardless of what Lisa might think, Joe's Passenger has always been very hard to understand.
But time and time again, Joe's Passenger has always been on Joe's side. When it came to emotional responses, when Joe asked for it to pull back on the favoritism after the Aegislash incident, ever since then it had been muting down the effect unless Joe asked for it. Whenever Joe is in trouble, Joe's Passenger is the first to help Joe out. And most of all, despite what some might think, Joe's Passenger never intentionally sabotaged him. Unintentionally sometimes, true considering the list above especially in regards with the Undersiders, but Joe's Passenger never tried to stop Joe from making friends and allies and from trusting his secrets (even Forge related ones) with his support network.
All in all, while Joe's Passenger may be flawed, it has always been Joe's ally. There's no doubt about that.