Illmatic

Hi guys, I'm an undergraduate biology student going into my final year this September, and I have been fortunate enough to help out in a evolutionary genetics lab over the summer. I'm even more fortunate in that I'll have a publication (middle authorship) by the end of the year, in the same lab. Until now, I've been completely oblivious to who exactly my PI is. Whilst he has always been quirky and difficult to deal with, I didn't think it was completely unusual - at least, not unusual enough for me to google him. Well, I did end up googling him around half an hour ago, and I'm shocked about the general dislike for him in the scientific community. I'm not unaware that he has made outlandish claims in his research, but I thought - given that he's a professor at a well-known, well-respected university - that he probably substantiated those claims with evidence. When I say people don't like him, I mean his work has literally been called absurd by a well-respected PI at a university that I wanted to apply to next year (this is the bit where I burst into tears). Seriously though, does this mean that the middle-author publication is essentially moot? He also knows me the best since he was my academic tutor this year, so I was expecting him to write my letter of recommendation too. If I do include the middle-author publication in my applications, how much will this effect my chances if I apply to schools where the PI dislikes him? Thanks.