I think that's part of it. I also think if he was 6'3" he'd have a real chance to be the first QB off the board in the upcoming draft, and he wouldn't be coming back.
Wilson/Manziel are changing the paradigm*, but it they will probably change it even more in 2013. I think Murray is clearly making the correct choice.
*(Gil Brandt, 79 year old ex-exec Russell Wilson doubter, recently inferred that Manziel will be a top pick in 2014, citing Wilson/Griffin as reasons why. Manziel's hype is his x-factor and Murray doesn't have it, but some of it might rub off on him if he puts up a great 2013 season and Wilson/Manziel continue to dominate.)