Things get worse in the B.C. Rail scandal

The Times Colonist reports that defence lawyers for Dave Basi and Bob Virk negotiated the forgiveness of $6 million in legal fees with deputy attorney general David Loukidelis and deputy finance minister Graham Whitmarsh.
That raises the perception the plea bargain had less to do with justice and more to do with closed door talks about money.
Most alarming though, is this sentence.

"But when special prosecutor Bill Berardino made the B.C. government aware on Oct. 5 that he had proposed to let the two men plead guilty, it fell to the deputy minister of finance, Graham Whitmarsh, and Loukidelis to figure out whether they would actually have to come up with the money, Loukidelis's statement read."

Why would the special prosecutor "make the government aware" of his plea offer? Special prosecutors are appointed in sensitive cases to ensure independence and avoid even the appearance that political influence was affecting the courts.
But if the special prosecutor is briefing the government of his plans, he is no longer independent. Telling the government of plans to seek a plea bargain, for example, invites interference. Either by proposing a different strategy or, as in this case, offering financial inducements to encourage a guilty plea.
This seems an extraordinary interference in what is supposed to be an independent justice system.