Frankly, given the horrific consequences of Wayne Enterprises's technology falling into Bane's hands, I think the United States of the Nolanverse is probably facing some pretty major questions about how much power it's allowed giant corporations to have and how little oversight they seem subject to. And I imagine that Wayne Enterprises and Lucius Fox are facing some pretty major legal reprecussions.
But Wayne Enterprises did government/defence contract work which is where most of Batman's gear came from (The Tumbler was for combat zone bridge building, the much of the Batsuit was body armour for soliders till the bean counters decided that a soldier's life wasn't worth $300k and the Microwave Emitter from Begins was designed vaporise and enemy's water supply).
So it's not a case of the Wayne Enterprises having too much power.
it is! Why on Earth was a private corporation allowed complete control over an arsenal large enough to seize control of the largest city in the United States? Why was it even legal for Wayne Enterprises to be developing a nuclear power device in the middle of a city larger than New York -- in a poorly-guarded, miniature facility? Where was the regulation? Who was keeping track of these things besides the company itself?
Those systems should have been dismantled or sent to the Pentagon, not sitting there in the Wayne Enterprises basement.
As for the theft well I don't think anyone would have really expected that combined with Bane having inside help otherwise it wouldn't have happened.
Which is irrelevant to my larger point: Not that Wayne Enterprises, Fox, and Wayne are responsible
for Bane's actions (obviously they aren't), but that they had accumulated too much power, and that the inevitable investigations after the fact into how the League of Shadows got its hands on that weaponry would almost certainly produce negative consequences for the company and for Fox, and would almost certainly expose Batman's identity.