You can set the NonInteractiveTranscript to be used when compiling and then set it back to the ThreadSafeTranscript when done.
Will not play nice with other concurrent users of Transcript so make this in an atomic operation...
Will allow you to catch the errors there.
There was a thread about having more than one transcript so maybe you can have your own for this. Is Pharo6 supporting that already?
Isn't the CodeImporter having what you need when doing a fileIn;? (Ok that means chunk format text but seems ok to me).
Phil