I personally felt the license agreement, and more so the language on the web site and download links, was always quite clear regarding commercial use. But more-so, I do agree with you, that it is a rather unfortunate change of course. My biggest fear, is that it will destroy the bulk of the creative efforts going into the 3D Warehouse. I personally get a great thrill out of downloading various space ships and crazy vehicle creations -- almost certainly the efforts of a 14 year-old boy somewhere out there on the internets. And there's no way they will be plopping down $500 to continue such endeavors.
So if I may, I'd like to offer my suggestion -- perhaps a $199 price point for Make? Or go even further, and offer something integrated with the 3D Warehouse -- so as long as you upload at least 1 model a month to the Warehouse, you can continue using Make for free.
More on the subject of your post, I feel it was a little naive of you to pursue a commercial business model off of the free software that Google was offering. I would recommend you stay with Sketchup, and contact their bulk sales department, to see if you could get some funding, and negotiate a good price to continue what sounds like an otherwise great business model.
--J