Given how long the last update took, I'm a bit concerned about future updates being even longer. The in-game decision MC makes after the hospital meeting w/ Tori basically turns LRH into two separate games (direct assault vs. sabotage). Sure some subplots could be shared (like bringing Kira & Spike onboard); but the main storyline of the game would take two different directions now depending on the choice made.
i think you're being over dramatic here
that decision will not influence a lot TBH, for the end off season it will affect :
1 or 2 scene's based on the season endgame(getting rid off the minon MC)
most off the the consequences for the alliance choice will play out in season 2 with the narrative change that the city officials (mayor de pasto etc.) will be the main antagonists.
possible paths from this choice i predict are:
will tori be a LI? (i can actually see her being with the MC could lead to possibly exposing de pasto as a fraud and replacing him with a more rouge favoured mayor,jessie existence would also be a possible narrative)
Getting Jaybird out off prison and the effects that it will have on candy's path.
aside from that you'd get a few initial favour points with the city officials in the new narrative but that would likely be balanced out in season 2.
maybe i left a few things out but i don't see how this would create 2 different story narrative's for season 2.