I honestly think it's one of those Yahoo/Facebook-type deals. If Apple tries to frivilously deny Amazon's app, they risk pissing off the dominant player in the ebook market, who could sue for all kinds of random things relating to iBooks. Prey lacks that leverage.
Exactly, so as I said originally, Prey is a much easier target than amazon. Also more people would be actively angry they couldn't read their books on an apple device than would be angry they couldn't use prey on their apple device.