In your case you will need to configure a program to filter the
events out before they get to fluidsynth.   I've never done this kind
of filtering so I don't know which software to recommend, but
assuming such a real-time midi filter exists, it should be possible
to create a chain by connecting the alsa ports of the various
applications together correctly and make this all work. 

Ken

    

Might be an overkill, but I'm quite sure pd (puredata) and sc
(supercollider) can easily do that - I wouldn't know the details though
(I just know how to do basic things with these two)

Renato
In Puredata it might be as easy as using the stripnote object which trips note-offs (zero velocity) from incoming midi.

Kind regards,
Lorenzo.