Personally it makes more sense to me as a simplicity issue. Developing a process to turn only one sex into supersoldiers is easier than modifying it to allow for the empowering of both sexes. There were some interesting excerpts posted here from Valdor I think about how the Emperor is relying heavily on regular scientists to develop the space marine program since he is splitting his attention between fighting/ruling/research. One of the reasons why the Primarchs are so important and their loss hits Amar Astarte so hard is that she wanted to I think have them as a template to refer back to in the event of shit unexpectedly going wrong in the space marines biology.

Basically the space marine project was an imperfect thing and keeping the process as simple as they could for the sake of avoiding errors strikes me doesn't trouble my suspension of disbelief.

Of course I recognize this is entirely an argument about fictional things in a fictional universe and if GW wanted female space marines they could have easily written things out in a different way.