Cooper was a Republican....

Yeah, it's not allegorical (no person or persons "represent" the HUAC, for instance), but it is applicable to that situation, that time, and the nature of blacklisting. But because it doesn't get preachy, it just feels real and true. As you say: it's human nature. In fact, because of this, a person might read a totally different message into the movie, warning about clumping into a group and forgetting the value of the individual (ie, anti-Communist!)

I found it to be a great movie, very nuanced, and the blacklisting thing didn't leap out at me until I was reading up on it later.

The film was filled with great characters and, yes, Kane's wife was probably the most sensible: knowing when to hold 'em and when to fold 'em, but also arguing (perhaps rightly) that Kane should just get out of town with her and prioritize her and their marriage above old debts and the village. Then again, who knows what would have happened to the town if Kane hadn't stood up to the criminal element moving in?

You're right: the Mexican lady cut and ran, but I did love that character. I got the feeling that she might actually have been useful in a fight, which made her boarding of the train all the more tragic.