Hopefully someone else can chime in to confirm that I'm correct, but I believe you'll need to place the Garrison and then sacrifice the Commander in the same "round" of room placements.
I'm 99% sure the game won't allow you to sacrifice the Commander before you place the Garrison since that would cut off that whole section of your chain and make it inaccessible, but if you place the Garrison and then open the temple without sacrificing the Commander you'll create a loop, your Spymasters will all shank each other, and you'll be left with even more cut off "islands".
If the game will let you sacrifice the Commander before placing the Garrison, I think that should be fine, again, as long as you also place the Garrison before opening the temple.
Like I said, I'm pretty sure that's all correct, but hopefully someone can back me up. What guide are you following?