im not sure if its possible to take off too much wax since anything left on top is excess anyway but it is probably possible to scrape some of your actual base off if you put to much pressure on it. when ever i scrape i usually dont get it ALL off anyway and just leave a slight layer to be taken off by the snow once i start riding.
First off, you should be using a plastic scraper. All of the plastic scrapers I have ever seen have been make out of polyethylene (I have one that I suspect might be polypropylene, but I don't have access to a GC anymore to check). HDPE has limits on its maximum hardness, meaning that it should be very difficult to scrape your board hard enough to damage to the base (without also wrecking your scraper simultaneously).
Waxing is half art, half science. Since karasene is fast becoming a wikipedia enthusiast, this entry should tell you most of what you need to know
Ski wax - Wikipedia, the free encyclopedia