You can use the tone_detect app per the wiki (
http://wiki.freeswitch.org/wiki/Misc._Dialplan_Tools_tone_detect) to detect the tone and act accordingly. You just need to decide what to do while waiting to detect the tone. Personally, I don't like doing too much call control inside a script, but YMMV.
Not having tried it myself I would suggest trying something simple, like using the tone_detect app to set a chan var and then have your script keep checking that chan var until your timeout has expired or it sees the fax tone.
-MC