Hackers and Junkers cooperate on a neutral basis, neither control the other's interests.
I disagree with you that the Hackers would not know of a Corsair-Junker liaison, strongly disagree, but it would undoubtedly depend on circumstances. If the liaison involved artifact trade inside Liberty, the Hacker solution would be extreme and effective. I don't see how Corsairs could maintain such activity. Corsairs don't have any power in Liberty, and the Junkers can't but wouldn't oppose the Hackers or Rogues. If I misunderstand, elaborate.
In terms of diplomacy, let me reiterate: it is not a problem that the Corsair stance toward Rogues is hostile, even if the reciprocal stance is neutral. The Corsair-Hacker diplomacy, on the other hand, is definitely all red.
Perhaps I should be more concise in this post: you have not taken any wrong steps in your role-play and your conclusions are fundamentally correct.