Might be a little late for an answer, but...
It seems to be somewhat tricky(even if in my last few play-thoughs I've gotten that result easily). However, you have to get the "HK-50 Core Upload Console" from a deactivated(laying on the ground like those you destroy) HK50 that resides in a small room, that should be on one of the sides of the area. Just search around, and you should find it.(This should be done before you touch either of the consoles)
Then, you'll need to go to the HK51 side, and use the console. Aside from the "Upload Hk51 schematics" option(which will give HK47 a few stat bonuses), the option that should be there is "Upload HK47 Behavior Core Template", which should then give a "Charge All Stations" option. After this, when you go to the HK50 console, and chose the "Terminate HK50 Production line" option, three HK50s will accost you, and within the conversation, a few 51's should show up, and enter the fight, helping you out.