So does anyone have any good ideas on protecting the 2 Faction sheets. They are only made of very thin cardboard and I don't see them surviving a lot of use. Is having them laminated the best way to go?

I would laminate

Honestly not too concerned about the faction sheet. It's not like you're going to be waving the thing around and moving it all over the place. It's a static element.

My battle board from my first copy of A&A has seen literally hundreds of games, and it got passed, moved, dropped, tossed, units put on and taken off, dice rolled on, etc...yet it looks like it did when I opened the box.

But yeah, laminating it is the best option if you are really concerned for it.