Yes, a civilian court can adequately protect intelligence, because civilian courts have ways to protect private information. Civilian courts can issue gag orders, and can also seal court records as they need to. Civilian courts do this every day all across the country. The NYC courts are up to the task for the 9/11 terrorists.
Civilian courts have procedures available to them to protect some of the most important commercial and sensitive information that exists. Financial and business procedures, patents, and all kinds of intellectual property are often disputed before civilan courts without valuable secrets being disclosed to the public. There is no reason to think the same would not be true of intelligence information.