Every single time this happens, a bunch of cry-babies come on and go "How dare they! I'm never ever ever buying another beer by X!" I think these people just come across as a joke. Does their logic really follow through to everything, though? Not shopping at Kroger, Safeway, Target, or their equivalent? Not buying products from Apple, Samsung, IBM, Microsoft, Sony, Dell? Not watching movies by Paramount, Universal, 21st Century Fox, Warner Brothers, Columbia, MGM? And on and on and on to every single facet of life. If you live a hermit's life, then fine, but you can't blame a craft brewery for taking an opportunity like this. If I were in their shoes, I would do the exact same thing.
Although I despise BMC beers, it's not because they're big and corporate. It's because I don't like the "American light lager" style. I wouldn't buy it if my favorite brewery made their own American light lager (though I might try it if I were at the brewery). I'm sure there are beers I like that aren't American light lagers that people would consider in the same vein as BMC, but there is no philosophy behind what I enjoy.
I support what I like, regardless of whether it's a local mom and pop store or a multinational conglomerate. And, sure, I've always really liked Lagunitas's beers (particularly Aunt Sally and Espresso Stout), but even if I didn't like them, there are tons of craft breweries that I do like that have been bought by much larger companies. And if ones I like that haven't got bought out did eventually get bought out, I'd still keep buying them. Besides, it's in no company's best interest to buy a company and change everything about the place so their fans stop liking it.