Practice the "butt sweep" as you sit down so that you are more-or-less sitting on the pleats flat rather than jumbled up. Hopefully it is a wooden pew and not one of those wretched padded monstrosities...mush easier to get things right on a smooth surface.
I've sat for good long periods and never seen a problem in either acrylic or wool kilts. I don't think you can generate quite enough heat to re-crease the pleats significantly. I never, however, wear a kilt when driving long distances.

"my fiance gets worried i am going to crunch the pleats"

You've just made a lot of fellows very jealous with that remark!!!