If I remember correctly, in the novelization, Spock did note that Kirk would likely escape from the brig if he put him there, so he marooned him instead. Spock Prime also had been on Delta Vega for two weeks, and had visited the base on DV multiple times (though somehow hadn't met up with Scotty. I didn't understand that when I read it, either... Why wouldn't Spock look to warn the federation? Unless communications were down, at the base.)
I think I need to find the novel and re-read that part. Anyone else read it? Help?