Of course they do... there have been no laws concerning the states having a militia. None, nada, squat. That's the point of the amendment: not personal gun rights.
maybe you missed where I pointed out that there is a significant circuit court split on this issue.
There are two main interpretations of the 2nd amendment along with a few nuances that won't matter for this discussion. First is that the right is a collective right of the states that allows for the state and federal government to regulate as little or as much (even up to a total ban) as it likes. The second view is that there is an individual right to bear arms which would mean that the state and federal govt. do not have the ability to regulate it.
The first view comes down on the side of government regulation, restriction and the ability to curtail individual liberty.
The second view comes down on the side of the individual and increases individual liberty.
The civil liberty interpretation would obviously be to support the second view which by the way has been gaining more and more acceptance. You are blinded by your own personal bias.
For a civil liberty union to side with government regulation and against civil liberty shows that the ACLU does not uniformly support civil liberty regardless of politics as you argued.