Can I get into trouble for writing a spy novel, and it just happens to be true?

Not really a legal question. And, easily solved by "changing the names to protect the innocent". Many, many novels are "based on a true story." So long as you provide suitable disclaimers this should be low risk. Remember not to falsely imply association with, endorsement by, or sponsorship of the source. Or, get permission and then you could call it the "official" version of the story. A lawyer would be a great help in getting permission.

The First Amendment should protect your right to write and publish this novel. Experienced authors in situations like this often confer with their literary agents and publishes about whether it would make sense to change the names of the characters and include suitable legal disclaimers in the introduction of the book. Further, if you are in possession of classified information concerning matters of foreign or military policy, knowing disclosure of such information could cause problems---the ongoing FBI investigation of general Patraeus and his mistress is focussed on the issue of whether there was a risk that General Patraeus had leaked classified information to his mistress that might be published. In most cases, you can probably make tell your story in a satisfactory manner--and make your political and social views known---without disclosing classified information. Certainly, however, disclosure of classified information can cause you trouble.

Probably not. Just don't defame a person, living or dead, and see an attorney to help you with the process. Should be relatively cheap.