hopefully soon enough Solo's Hl: Enhanced.
This is already possible using GMR (Game Model Replacement).
In "hlenhanced/models", create a folder with the same name as the map (if your map is "the_core", then the folder has to be named "the_core"). Inside that folder, create a text file with the name of your choice (I'm gonna assume "female_sci_gmr.txt"), open that file with your favorite text editor.
To replace the HL scientists by your female variants, you would add in the file:
The quotes are VERY important so don't forget about them, you may save and close the text file when you're finished.
Open your map in Hammer/Sledge/J.A.C.K. configured for HL:E, go to "Map's properties", in the "Global Model Replacement" field, just type the name of the GMR file you created earlier ("female_sci_gmr.txt").
Compile the map and HL:E should change the HL's scientists models to your variant.