Weller informed his colleagues that if they stayed the course, they would undoubtedly risk legal repercussions and hurt their case for exonerating themselves.
Jane, Weller, and the formerly shaky Zapata were on their way to stop Ivy when the interim FBI director gave a direct order to stop the operation.
They all collectively decided it was too big to back down on, and went ahead anyway.
If there’s any upside to this, it’s that Jane likely spared the rest of the city a cruel fate, and won’t remember that the FBI team may be screwed anyway.