I think it would be akin to "enabling" more bad decisions on the part of the owner, unfortunately. With so many other options in comics, I would not donate to a LCS unless it was out-of-this-world special. I'd also have to know that the owner could RUN a business, which in this case would be doubtful.
I *have* thought about saving some of my favorite restaurants, however! There is a local brick oven pizzeria that has great food, but the owner is a horrible businessman. I root for his success, but drive past everyday expecting to see an "out of business" sign on the door. I guess I feel a little differently about one-of-a-kind products, like a specific meal or dish or service.
Comic shop? Probably not.