This question has been around for awhile with no takers. A few thoughts that might help, emphasis on "might".

I've fiddled with Mozrepl before, but its been a long time ago. I don't know of anyway to tell it not to do what it wants to do with STDOUT.

You can of course re-direct STDOUT from your script to the "bit bucket". On Unix, I think this is dev/null. On Windows there is a reserved file name, NUL that serves the same purpose. program.pl > NUL sends output of program.pl to nowhere.

It is possible to make a detached process without a command line window. On Windows, see detached Tk process. This is a technique to get Tk started without the annoying command line window. If the window isn't there, then of course users won't see any messages printed to it. I think you could launch your program without a command window.

Again, I don't know of any way to interfere with MozRepl's use of STDOUT. Both ideas above just have to do with throwing away what is written to STDOUT.