SPOILERS. The hidden text below assumes that you have made to the quest "From Within". Note that this is as far as I have made it in the game, so please do not post spoilers about things that occur after this. Thanks!
As a father with 2 young kids, I have felt compelled to not deviate from the main quest and pretty much go straight until I find my son. When I got to the point of needing to build the teleporter, the only logical choice to build such a huge and technologically advanced device is to use the BOS (lol at the railroad or Sturges trying to build that thing). If you use the BOS to build this device, you are given a quest automatically to talk to Doctor Li and convince her to rejoin the BOS.
After the big reveal in the Institute, I have decided I do not want to help the BOS, but I am forced to talk to Doctor Li as part of the Institute as well. The problem is that I have no choice but to convince her to join the BOS, which makes no sense as the story should be dynamic based on the information you learn. Is there anyway to choose NOT to do this quest, but still talk to her as part of the Institute introduction quest?