I think the real criticism around flipping companies has more to do with the fact that it is (generally speaking) a fake economy. When companies, with no revenue (or more likely - negative revenue) are getting acquired for (up to) a billion dollars, only to be shut down after the founder's stock vests (or sooner)...it makes the whole startup world look a like a Ponzi scheme (as Mark Cuban said, in so many words). Get popular founders, get popular angels/investors, get users, get money. The only person who really gets screwed in that equation is the stockholder of the public company that acquired something it intends to shut down in a few years without recouping any of its investment.
Presumably the stock holder of said company could sell their stock and move on. Personally if I were an engineer at such a company and saw my company 'wasting' all this money on what are essentially big signing bonuses I might be pretty upset, after all you can't easily sell your 'stock option' until it vests.
That said I wonder if this will correct toward a contract scheme ala national sports, where the 'engineers association' starts negotiating 1 - 5 year deals for 'star' players. It seems it would be more efficient economically.