It's not so much a potential to be gamed, as encouraging people to post without thinking things through, as well as misleading readers as to which arguments are correct.

I'm not sure that's true. As I originally said, the first comment in a thread often gets karma of greater absolute magnitude. Bad posts get voted down more harshly as well as good posts getting voted up more. I think the higher readership for top level comments explains this. It means that from a karma-gaming perspective posting a top level comment is only a good move if you are confident it will be received positively.

In a case where a comment is both funny and incorrect, I think we should prioritize the correctness.

How about other attributes not directly related to correctness? How should niceness be judged relative to correctness for example?

I still think there's a conflict between you wanting people to give more upvotes to things that are correct but fewer to things that 'agree with the majority opinion'. I don't think people upvote because a comment 'agrees with the majority opinion', they upvote because a comment agrees with their opinion. That tends to produce greater upvotes for the majority view. In your second example I think the greater upvotes for James Andrix reflect the fact that he is more correct. Your real complaint seems to be that the majority opinion is wrong on this issue. The best way to fix that is to make a better argument for the other view, not to complain that people are failing to recognize correct arguments and upvote them.