What streak? The game before Augsburg they beat Barca, two games before that they beat Inter.I don't think you can decouple these things. Going on that kind of streak always has its effects on the dressing room and you often don't hear about the exact details of what's going on behind the scenes after at least one of the actors has left the club. Also, it's not like Nagelsmann has been completely unassailable so far. Still, I agree with you that Kovac should have never been appointed in the first place. Some of the stuff he said and did just seemed weirdly out of place for a Bayern manager.
Rumor was also that Lewandowski wanted to leave, because Bayern showed interest in Haaland. A lot of BS was spun during that saga, who knows what was true.Rumour has it that he already lost Lewandowski and that that was a cause for why he moved to Barcelona. It's not hard to imagine other players to lose their trust in Nagelsmann as well.