This person, who worked for Six Apart during the Strikethrough crisis of a year or so ago, has presented a reasonable alternate explanation for the removal of LGBT books from the sales rankings.
Hir theory is that a large group of conservatives have been manipulating the Amazon process for flagging "objectionable" content, rather than Amazon putting into a place a policy that deliberately removes these books from the rankings. If this is true, it's not Amazon that is the homophobic villain.
That said: whatever the reason for the books to have been removed from the rankings, they need to be reinstated. If it's due to a homophobic policy by Amazon, the policy needs to be changed. If it's due to a crusade by an anti-LGBT group then Amazon needs to find a way to prevent its policies from being exploited.