Who's to say what James knows and doesn't know? He wasn't born in a vault, and the Brotherhood of Steel knows its history with them. At any rate, I'd say it' pretty safe not to trust a force that arrives by helicopter with guns blazing, led by a man who just shot one of your researchers dead in order to get you to comply with his demands. Not to mention the dubious propaganda on the radio. That post ignores the fact that the Enclave want to use the purifier to genetically purify the wasteland, and failing that take control of its most valuable resource.
Zero ill-intent? Are you sure about that?