Additionally, I'd like the files to be binary to discourage casual browsing/modification from other team members who might fiddle with the file with good intentions but not understanding what they're doing.

I thought that file was encrypted anyway? If so, the obfuscation is really superfluous.

Or do you want to encrypt the passwords in that file, but not the file itself?

I assume that the credentials file isn't very large. If that's true, you can store your login informations in something as simple as YAML or Storable, encrypt the whole thing and dump it to disk. In the other directory you read and decrypt it, and let your de-serializer handle that string.