Ben,
If the EL90 transmits any kind of MIDI message when the paddle switch on the swell pedal is closed, the Hauptwerk can map this to the Crash Cymbal. I am using a Yamaha HX-1 and the footswitch does not trigger any MIDI events. It will be necessary to attach a third party MIDI encoder.
A very inexpensive option is the X-Keys Strip. This would give you sixteen programmable buttons which could be used for pistons or thumb buttons.
http://www.xkeys.com/xkeys/xkstick.php
Joe