See this op-ed that was published in The Hill and shared by Claire Rubin, Homeland Security is too important to leave without a leader.
Everything printed there is right on the money. DHS has many moving parts and each of them can, depending on the situation, be front page news when bad things happen and things go wrong. I had hoped that John Kelly was going to be the guy that brings better morale and efficiencies to the department. Now the search must commence for someone new to perform those functions.
As for the remarks about the budget cuts. The new secretary, whoever that might be, has to defend the proposed budget. It is not like they can come in and say, "The President wants this, but I think we should do something different." The time for that discussion was when OMB was making up the budget and proposing cuts to grant programs that we have become addicted to.
Now is the time to pray for someone good to be appointed.