What you are describing are the provisions Congress has made under their authority in Article I. They have created a legislative definition of "militia" (10 USC 246) that is restricted to male citizens. Female national guardsmen are the only women that fit within this legislative definition.

I think we can agree that Congress is fully empowered to change its legislative definition. We would probably agree that the current definition is unconstitutionally sexist and ageist. Congress could change their age limit from 45 to 60, and remove their "male" limitation. They could expand their definition to include a very, very broad range of people, if they wanted to. They probably couldn't expand it to include 8-year-old kids or quadriplegics; the court would probably rule that sending kids and severely handicapped people to war is unconstitutional, but they can certainly include far more people in that legislative definition than they actually did.

Constitutional rights do not originate from legislature, and cannot be revoked by the legislature. Congress can, indeed, change the legislative definition of "militia", but they cannot change the constitutional meaning except through an amendment.

So, if Congress could rewrite its definition and compel women to register for the draft tomorrow, then women were members of the "Well Regulated Militia" yesterday, and 200 years ago. Congress's failure to provide for calling forth female members of the "well-regulated militia" has zero impact on the rights guaranteed by 2A.