I'm not sure how to disable the flash (it's actually your screen going white) but I came across this app today, which might do what you are interested in:
iGlasses:
"Adjust and manipulate your iSight video settings from within iChat AV and many other programs, including iMovie, Photo Booth, Yahoo! Messenger and Skype. iSight too dark? It just needs iGlasses. Apply easy preset settings and fun effects to your video conferences and recordings."
I've downloaded the trial version and the night vision feature might be the closest thing to disabling the 'flash'.
Hope that helps