Pains me to write this as a big fan of Castle and Fillion, but something about the show just isn't working for me. Feels very formulaic/paint by numbers with little innovation and a diversity checklist/agenda. I'm normally the one to call people out for grasping at SJW straws so I don't think that's what I'm doing here, and it's a lot more than just how overt the 'militia' part of that prison break episode was.
But holy shit I think the single most glaring thing has absolutely nothing to do with any of that, and it's how badly they pissed away Mercedes Mason's stellar performance as Captain Andersen. When Captain Montgomery sacrificed himself in the season 3 finale of Castle, it was very upsetting because of how well set up the twist was and how long Montgomery had been with us. When Captain Andersen has a major badass moment interrupted by a blind neck shot from a fleeing perp, I honest to god rolled my eyes at how out of place and anti-climactic it was.
Regarding the cliffhanger, it's almost certainly just a reaction to the experimental vaccine he was injected with, second most likely possibility being the chair to the head from earlier in the episode. There's no way they start season two with him slowly dying of hemorrhagic fever in a CDC tent, and I think it's unlikely they were planning to write him out after a single season when they didn't even know if they would be renewed.
Hope the show does better in season 2 and ends up with a decent run, but I doubt it can last too long without some major nonsense seeing as how the show is called 'The Rookie' and the first season got us almost half way through his probationary period.