Do you have any evidence of that, or are you just saying 'of course Amazon must have done something'? I use goodreads and haven't noticed any changes that would cause that.
I have - mainly for Audible - I've noticed some commenters noting how there's only interest in a given book (in this case, the Arawn Cycle) because Audible did a sale on the series.
Most people aren't active readers. Goodreads users are active readers. Amazon bought Goodreads (and other sites like Shelfari) because that's where the readers are.
I read 74 books so far this year. Most of them were purchased from Amazon.
Also, Goodreads has an active review community, and good "by reader" data for recommendations (as opposed to Amazon's "by account" data. If Amazon were smart, they'd be working very hard on improving recommendations with their Goodreads data.