Can I substitute pureed green tomatoes for the zucchini in these cookies?

AntoniaJames is right, but you might want to try some experimentation -- the idea is promising. Perhaps you could oven dry the tomatoes (you can find some instructions on this site, or others) to reduce the moisture. Then there's a question of acidity -- you'd have to balance the tastes.
How about some kind of tart? I think they'd be delicious that way!

i wouldn't. The texture and moisture levels would be so different. ;o)