No...I wouldn't take the fish out. And depending on the water conditioner that you use to treat the replacement water, they should have a stress coat or other additive (maybe) to relieve the stress that the fish go through. I use a vacuum when doing PWCs, and the fish don't mind it so much anymore. I think they get used to it after a while.
Edit: I mean a gravel vac...not a vacuum...lol
My life revolves around food. Feed the kids, feed the hubby, feed the public, feed myself...then there are the fish. Who's begging is just priceless. Who would tell the bubble poppers no?