I also feel that the Vajra aren't "hostile persé", they seem either influenced into fighting humanity or they are afraid of humanity. (btw I find it funny how alot of people started to link the story with Ender's game after these last few episodes. Frontiers story does feel familiar to that series).
I think the "grace/Bilrer" faction is responsible for the manipulation sofar (going back as far as the 117th research fleet) and that the galaxy is also linked to this (liked the theory of galaxy beeing taken hostage by "the faction", but rather expect it to be staged as a whole by the galaxy crew). From Bilrer's point it seems like an awsome way to make money and from Grace's point ... well I have no idea what she is in it for .....
Im sure they're after the crystals and the Vajra's fold techniques or that they were atleast trying to make weapons out of the Vajra (my money is still on the two critters ((Ranka's and the one from the swamp) to be original Vajra, pre-manipulated). The Vajra seem like a test weapon gone wrong.
I actually felt sorry for the Vajra when Ranka started crying at the end of 14 ... somehow it felt as is some small bugs were getting stepped on and it felt really sad to see them getting wiped out like that.
Who knows they might turn out to be good in the end