Off the top of my head, they make those large metal gate looking things that keep your dog from jumping into the front of the car from the back. You could always measure for the size you need and purchase one of those but simply place it in the back of the vibe effectively blocking the dogs off from the actual hatch completely. You could then even open the whole hatch and they couldn't escape, though you probably wouldn't want to leave it open like that if you're not around. (I trust my dogs, but not people. lol)
Another alternative would be to find some sturdy screening or netting and install it across the rear hatch window. WHat I have in mind would involve screwing in a couple anchors or what-have-you for the screen so you have a place for to anchor it securely when in use. You may even get away with some hardcore velcro strips but I'm not sure how secure you need it.
Perhaps I'll have some idears tomorrow. Keep us informed!
PS - I feel like having your windows and sunroof open (provided sun isn't pouring through it on a hot day) would be enough air flow for any safe temps or amount of time they'd be stuck in there. If you NEED to have that back window open, I question their safety. However, if they are safe as you assure us they are, then every little bit helps.
PSS - One more thing. Do you have one of those windshield visors? I use a silver reflective one and not only does it keep temps down but protects your interior. Being someone who's lived in the deep south and the desert, I've learned to love these things. Remember, even on a cloudy day, UV rays heat your car and ruin your interior.