Plans Within Plans Within Plans
Starfleet gave command of the
USS Murgatroid to Commander
Storvik for a variety of reasons. All of those which they'd discussed with him were true. It was also true that, as Storvik suspected, Starfleet continued to be influenced by stereotypes about Vulcans when dealing with him. They were surprised when he decided to maintain the status quo on the Murgatroid. Even though he had played a large part in creating and maintaining that status quo in the past, they naturally assumed that (as a Vulcan) he would want to implement discipline and order once he took control.
But none of that mattered. There was at least one other reason for placing Storvik in charge and encouraging him to keep Doctor
Mib Khan and Counsellor
Lothar in his crew - a reason which they did not discuss with the Vulcan. The Murgatroid, along with the aforementioned officers, are bait. Bait for
Evil Janeway.
Since the Mirror Universe analog of Kathryn Janeway had actually attacked Starfleet Command where they live and work, they are exceptionally scared of her and keen to eliminate the threat she holds. They know she'll want revenge against the Murgatroid and her officers - they are correct in assuming that she was behind their recent attack - so they want to leave the Murgatroid and her officers out there together, to draw her fire. Presumably, once
Evil Janeway is drawn out into the open, the Murgatroid or Starfleet will be able to deal with her. If the Murgatroid, freak-show of a starship that it is, gets damaged or destroyed in the process - well, that's a price the Admiralty are willing to pay.
Especially since none of them have a nephew in the command chair anymore. Admiral Edward Jellico went along with this plan - endorsed it enthusiastically, in fact - because his nephew
KY Jellico is not to be part of the "sacrifice". He assumes that his nephew, having retired, would no longer be of interest to
Evil Janeway, if she was even aware of his departure. KY Jellico had already arrived at his retirement home, a "safe, calm world in the middle of nowhere" - he was unlikely to know or care if anything happened to his former shipmates.