If you use iTunes it's super easy to go into the track settings and tell the track to end before the applause. No editing program needed. I guess I'm indifferent to the applause. I don't like them changing the album but I also enjoy a little peak behind the curtain of my favorite album.
I guess I too have always felt the need for a little sense of piece at the end of Together Alone. Back in the day I actually added the wave sounds from the end of "Zen Roxy" to the very end of the title track. So there would be this cacophony of sound and then just quite waves fading slowly away.