I very much like your thoughts on why the Doctor simply couldn't see option 4. I've seen a few people unhappy that he couldn't see the solution because it made him seem stupid that he needs Amy to solve things. (To that I wonder what show they've been watching since that's the very reason he needs a companion - besides the the whole going nuts thing - they see things and solutions that he doesn't.)

Also, from his point of view, why would the whale stay when it has been tortured? He's disgusted with the humans and it makes sense that the whale would be too!