And if the fire didn't kill anyone, what would be the point? Destroying a headquarters won't prevent the organisation carrying out its plan.
Besides the fact that, as oers said, he wasn't Batman at that time (and has maybe not thought that philosophically about killing people yet), the only reasons for doing this are not just to either kill anyone or destroy the organization.
The most obvious reason for starting the fire was to make distraction and chaos, which enables him to escape. I would say he was at a dead end and needed some way to get out of it fast, so starting the fire was a good chance for enabling his escape. He probably didn't think through that fast if anyone would get killed in this fire, he just needed to escape. He didn't kill anyone on purpose there.
I believe that the definitive answer is no, he did not break his code about not killing people, the reason being is that he didn’t intentionally kill them with his bare hands. As we see near the end of Batman Begins, he has no problem with letting Ra’s Al Ghul and his clan die in the crash. He even stated
"I'm not going to kill you, but I don’t have to save you."
So this brings us back to him blowing up that building. He didn’t intend for any prisoners to be killed, he was just trying to escape. Since he didn’t directly kill them, it doesn’t break his code.