Naruto had prior knowledge and sage mode, and still would have lost if pein actually WANTED to kill him and not bring him back alive to extract the biiju. Naruto barely cranked out a win, and only did so because hinata sacrificed herself for the sake of kn6 rage mode.
Bee would be overwhelmed and crushed... on top of that bee has no answer to the dog summon
People need to remember that SM Naruto was not a match for Pain on his own. He had extensive intel gathered by Jiraiya/Kakashi/etc., three giant toad summons (one of which held his own against a weakened Biju), interventions from Fukasaku, Hinata, and Kurama, AND the fact that the most powerful Pain was out of commission until the others were taken out, AND the fact that Pain was trying to capture him alive. The gulf between their abilities is so massive it's actually ridiculous. Killer Bee is definitely stronger than Naruto was at the time, but that's not even close to being enough to defeat Pain--he loses every single time.