Because in Doctor Who, the rules function according to what creates better drama, and the parting of the Doctor and Amy/Rory was thematically appropriate, foreshadowed, tied up an interesting character arc, and allowed the story to progress. Doctor Who is filled with enough crazy, wibbly wobbly timey wimey stuff that you can throw a whole bunch of random gibberish out there and still seem credible as long as it serves the story. Looking for plot holes is kind of like questioning why a king would be so invested in saving an egg that fell off a wall. It's easy to not look for plot holes, and it makes the story better, more enjoyable, and more meaningful when it has that leeway.