Ms Blake is working with Deucalion. The choice between saving Scott’s mom/Stiles’s dad is a false choice and just a means to propel Scott to do what Duke wants him to.
I had the same thought because the situation in the hospital seems to be so staged, like a virtuously designed trap that leaves the hero with nothing but bad choices. But if this is all a giant conspiracy, what would the darach need the sacrifices for? Also I think it is way too complicated (we are overanalyzing again, getting all excited and the resolution will probably turn out to be underwhelming and predictable) because seriously? If Deucalion really has studied his object of desire (and I am pretty sure he has) he knows that he does not really need this huge setup to manipulate Scott into doing what he wants. Scott’s weakness (and also his strenght) is that he cares so much about others and would literally do everything to save them. Even join his little all star pack if he has to. Deucalion would not really have to go to these lenghts to get what he wants from Scott.
Still I think it is very suspicious that the Alpha pack did not seem to be too disturbed by what the Darach did up until now. Jennifer committed one ritual sacrifice after another and Aidan and Ethan did not even seem to know what was going on. Deucalion on the other side obviously knew a lot, which included the exact location where Deaton was strung up, and still did not seem to be too inclined to do something about it. If he knew what the Darach was up to, why did he watch her getting stronger and stronger? He just observed and did nothing.
So it is pretty weird that now suddenly they are all after her. This does not make sense. It is only plausible if indeed there is a personal connection between Deucalion and Jennifer nobody- not even his own pack- knows of.
I should probably stop thinking about it because I get more and more confused.
In other words: I smell giant plotholes….