I've personally been in Microsoft's "let's give developers everything for basically free" programs since 2006, and am not worried that I'll suddenly face a crippling bill down the line.
Shafting little startups for a lousy grand or two really is not their business model. Think about it for a second and it'll make sense.
EDIT: To be clear, I'm not advocating gambling your business on Microsoft's goodwill here. For the same reason I don't advocate building a business that a single bill for $1,000 can kill.
The worst case result of MS pulling the rug on all their BizSpark-esque programs is an extra couple thousand dollars a year in the expense column. Here's hoping nobody here works for a shop where that would be a big deal.