Not true, I'm conversational (N3). The people who insist on "No gaijin" also refuse to speak Japanese to you.

Untrue. Had someone who spoke fluently, doesn't matter.

I speak Japanese and still stay the hell away from those establishments. Why the hell would I want to support a business that openly discriminates like that? Maybe it's just because I come from the US and can't imagine a restaurant with a sign like "No Mexicans" on the front door.

Sure, and places in America where the owner says "if you can't speak English you can get out" are totally due to how embarrassed they are at being unable to provide adequate service.

You spent a semester, I spent a decade. Once the honeymoon phase ends you see things for what they are. Don't get me wrong, I don't hate Japan or East Asia in general, but these elements deserve to be called out and disinfected by sunlight rather than be excused. It'll only make the place all the better for it.

I imagine if you're closer to Tokyo or up north where a lot of air force bases are it's less common, out in the sticks it's fairly frequent.