My opinion is that it's reasonable the way it is, and it probably works the way people would expect. And as Fillip pointed out, if you think about the option as "Yes, I want to exclude this group" then the inheritance works like you say it should.
However, you have a point. If the "sense" of the option were reversed so that you were choosing which groups were allowed links, then it would be useful for forums that wanted to sell that feature in a paid subscription. (Edit: yeah, it can still be done using primary groups, but I think the reason secondary groups exist is because it's easier to manage "add on" permissions). I had never thought about that myself, and I'm going to consider that in the future (well, if I ever develop another mod that is

). But that doesn't make it wrong, and it looks to me like you were given a reasonable reply.
You guys need to stop bickering. Don't post anything else that isn't related to the question.