The problem is that SWTOR is an MMOrpg. If this were a standalone game then indeed they could remove the gender checks, do some VA, and release a patch.
But. This isn't a standalone game. Nor a standalone game with multiplayer options. This is an online game. Live at that.
They can't just go back and change these options. It would likely bug everyone's progress with their companions in the process. The same goes for NPCs. They can't just change those. It'll have different effects for people who've done the quests, are in the middle of the quests and those who have completed it. And these conversations and quests can't just be reset either. And the idea of some item resetting it, is also nearly impossible. It can be coded, but the consequences and bugs as a result cannot be overseen.
The problem with SWTOR is that SGR could've easily been in at launch without much difficulty or high costs. Instead someone made the poor call to not do it. At an executive level maybe they thought like most do here that it would be easy to implement, but are now realising that it's not an easy task, but an incredibly difficult one. They'd be facing possible bugs for almost every quest and conversation. That's an impossible task.
The only thing that can reasonably be done is adding new companions the way HK51 has been added with VA for the earlier planets included. Additional quests can be added on the core planets with NPCs that are available for SGR.
Your game, your character and progress, are on the server. This isn't a standalone game. It's coded differently. It's not something that can be fixed easily.
Additionally, to implement such a patch for the millions of account toons that are the servers, they'd have to take the servers down for days, not just hours. Adding new content, some new code to add new FPs, WZs or Planets already takes 4hrs for a small patch, and 8hrs for a big patch. Now imagine them recoding it all, and making changes to save games. That's a task that'll take days, and sorry folks, just not realistic. I would love to see it. But realistically it's nearly impossible. At this point in time I'd rather see them spend time on some new SGR companions. That can be a content patch done in an 8hr server downtime. Development won't take much longer than redoing the previous companions, and it'd be something new for everyone. Yes it'd be the "SGR companion", whatever. It's something that'd get me through the 50 levels for a toon before I reach the new content that will be inclusive.
I don't believe is so monumentally complicated. I bet one tab of your cargo hold has more information than whatever flags one of your companions has.
Changing the script to companions story arcs could be just like changing the workflow of whatever in a ERP system (probably much less complicated). You add alternative paths, steps, new conditions, etc.
In this case, it'll be only a new path. The "friend" path and the "straight" path will be the same. If someone has their companion's story already in progress, there should be an option to go back to square one. Can't be that difficult, since they dont have an impact your class story, nor or the world.