Chances are that Locke has made an error - after all, he wasn't with the survivors when Naomi dropped in so chances are he thinks they may just have the boats rather than the helocopters (I've probably forgotten him talking about the 'copters somewhere along the line.)
But if he wasn't going to be safe in the Barrack's then why would Ben have gone with him? Sure he's proven himself repeatedly capable of manipulating Locke and Jack's obviously in a trigger-happy mood but if he wanted to survive and there was any safer place, surely he'd have spoken up and made sure that Locke took him there?
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