Hi Nancy: I've been using rubber cement on my applique quilts for 25 years and haven't had any problems - but you are right - it doesn't smell very good while applying it. It works well because it stays flexible and 'releases' when you want to remove the freezer paper. I've recently discovered 'repositionable' glue sticks (Scotch brand, Lapel Stick, and Sewline) and they work very well also. The big thing is being able to remove the freezer paper which is why ordinary glue sticks won't work - once they are dry it is a permanent bond.
I hope that helps allay any fears about using rubber cement but if you'd rather something that's a little less smelly go for the above mentioned glue sticks. Cheers, Sharon Pederson. P S - you can't get it in the UK (I had to ship some ahead when I taught there).