My DH painted the entire inside of our house while i was pregnant with DD, and then painted the kids bedrooms when I was pregnant with DS.
Like everyone else has said, just make sure you have plenty of ventilation - doors and windows wide open. The onions in a bowl of water in the room helps too...it soaks up some of the smell somehow?
You can also get low odour paints as well.
Maybe also when you guys are pouring the paint from the tin to a tray or smaller pot, do it outside/away from where you are painting, that way you don't have a big 10 or 20 litre tin sitting around creating even more fumes.

Hoenstly, i don't think the water based paints now days are that smelly. I'd be more worried about sanding back old walls/ceilings that could be ridden with asbestos or painted back in the 70's - 80's with lead based paint more than anything.