That said, were it my brewery I would not fill other's growlers (or would put stickers over them). That's just common sense when running a business.
Are breweries in the glass selling business, or the beer selling business?
It's also about image and branding. You can make great beer, but to sell it well you need people to know where that great beer came from. I can totally understand this.
A better way to deal with this, however, is instead of slapping a sticker on someone's property, get custom-made brown paper bags with your logo on them, and put the growler in that after filling. It's a fun image, you get the branding, and the customer doesn't have the annoyance of either not having a growler filled or having a sticker put on his glassware. It's like this: http://revbrew.com/store/product/5001
except in a paper bag.