I have a different take on why Miller went to jail. First of all, Fitzgerald needed her testimony to prove that Libby had told her about Wilson's wife. He probably was also trying to get her to incriminate Cheney as well.
Additionally, an unstated reason for showing no leniency to Miller is that she accidentally tipped off the head of a charity that was funding Al Qaeda that Fitzgerald was going to raid their office the next day. The charity went to into overdrive destroying documents. Fitzgerald indicted the organizations leader but was not able to get a conviction. One of the biggest blemishes on his record.