Disassembling crank on a 2006 Trek Pilot 2.1
I would try reinstalling the drive side and non drive side cups to the frame (to keep the spindle centered).  Then I would recommend a game of whack-a-mole on the spindle with a rubber mallet.  I have often had to remove a crankset this way.  A rubber mallet should be in pretty much any home mechanics tool kit.  The rubber mallet has almost no chance of damaging the spindle.  Provided you don't smash/dent your frame with it, it should be fine.

With the cups on tightly and nondrive side crank off, you may also try rocking the drive side crank arm back and forth some as you rubber mallet the spindle.