Actually the fps shouldn't be much different because it only changes one equation slightly. Specifically from:
0*smokeColour + (1-smokeAlpha)*destColour
to
smokeAlpha*smokeColour + (1-smokeAlpha)*destColour
where 1 alpha is maximum transparancy and destColour is the colour currently in the colour buffer. Looking at the equation makes me strongly think this is what it was supposed to be. The original smoke is black not because the smoke texture itself is black but because its colour is being nullified by the zero.
I tried it on end
but I had to double my r_particles_count again to get the full effect because only half the room was emitting smoke lol. It looks cool but was quite slow on my machine as you can see
Original:
http://img35.imageshack.us/img35/4250/end001.png
http://img194.imageshack.us/img194/760/end004.png
Modified:
http://img35.imageshack.us/img35/7923/end000.png
http://img5.imageshack.us/img5/4480/end005.png
There's also gl_surface_lava 4 which seems to triple the number of smoke particles
http://img40.imageshack.us/img40/3103/end002.png