The God Complex farewell scene was not intended to be a goodbye, so even when it played out I knew it was only temporary, so frankly it didn't count. I'd already seen the publicity photos from Wedding of River Song, and BBC America and Space kept Amy's introduction.
In my opinion it was just a "bump in the road" the same as Tegan's apparent departure in Time-Flight, and a means to an end in order to set up the 200 year gap leading up to the Doctor recruiting the Teselecta.
re: naming the perfume. Considering no one actually knows what petrichor means, its real definition is meaningless so she could have picked the name simply based on its sound. And considering we live in a world where wine critics consider a wine to be good if it reminds them of things like barnyards and Band-Aids (actual terms I've seen used in reviews), "smell of wet dust" could be a positive term with regards to perfume!
Alex