Based on available information, with an understanding that further data may influence this opinion...
I am pretty well convinced that Flores' interview was a sham in the sense that the Giants had already decided to hire somebody else. I don't think it involved conscious racism, if it involved racism at all.
In their shoes, I would have responded to his accusation the following way:
1) It is true that we had already decided to hire somebody else. The Rooney rule requires us to interview, not to hire, minority applicants. And we did not cancel our interview with you upon our making that decision because of the Rooney Rule, but also because we anticipated this sort of accusation.
2) We also interviewed you because we wanted to hear what you had to say about what you would do. We were sincerely curious about your thoughts and thought it would be a cheap way to pick your brain. Obviously, we were wrong on the latter point - the cost is far higher than we expected.
The claim that the Rooney Rule is racist is laughably wrong-headed but, as already posted in tother thread, totally predictable. Affirmative Action efforts are a response to endemic racism.