I like to start off with that I really liked this book yet I do get the controversy and I think it is unfortunate.
On the one hand, I get that it sucks - and might even be dangerous - to sort of create a message that girls who are gay are just in a phase and that phase will be over when they meet the "right guy". But that is not at all what this book is about.
I feel like we should look at this book as Ramona's personal story and like life becoming aware of one's sexuality can be messy. It is emphasised in the story multiple times that Ramona is not "turned straight" by Freddie.

Spoiler

And at the end, even Ramona isn't sure about her sexuality

And Ramona's story is so much more than that. A big part is about her family and her future. So don't be too quick to judge this book for its synopsis.