[boomboomsubban]

>Is it a violation of Country B's autonomy for me to decide to not to trade with them because they are trading with country A?

Yes.

>am I violating the autonomy for all of those countries?

Yes.

The clearer example would be imagine country A attacked me, would refusing to trade with country B violate their autonomy? And the answer is still yes, but both country A and B are already violating your autonomy so it's a justifiable violation.

With your example, I wouldn't say producing weapons clearly violated your autonomy, but that's a completely different argument.