Are you using Vanilla FRED2 or FRED2_Open?
For FRED2_Open, what you could do is set the Music to "None", and tell FRED to play the music file by the file name via a sexp, then when your done, stop the music and sexp change soundtrack to whatever you want later.
Or, try checking ignore for counting goals in all the ship orders. I have no idea how that would work though.
Or, modify the music tbl and replace the victory music with the ambience. You'd have to make do without any victory music at the end though. (Unless you changed the soundtrack with FRED2_Open.)