Ah so that area is locked.
Basically, you need to fight the Queen. If you win, the story will continue as normal and there will be no issues.
If you lose, you will get experimented on (the virus effect will increase dramatically) and then get booted out. If you go to return to the castle, the door is now locked and your key won't work. But the sewer path there you showed will be open so you can head back into the castle.
So essentially, if you fight and beat the Queen, you don't need to worry about that path at all.