I think think yes and no, depending from the POV. On day to day procedures and other decisions that need a background on how the agency does business, the career employee is the best source for an intelligent decision. A mirco-managing outsider with no institutional knowledge is a liability. Often they want to change the arrangement not because their idea is better but just because "we did it this way where I came from". The upshot is the chiefs get miffed, retire or move on, the clueless exec is gone in four years and the agency is gutted of all experienced managers. A good new exec should observe the situation fully before bringing in the big changes.
On the other hand if you have someone coming in with a mission from the administration, I think the key is communication from the exec to their top managers. If the exec describes the result they want and can listen to their managers' ideas on how to achieve it, a lot can be accomplished. A good exec can let the managers handle implementation details and not interfere by "getting into the weeds". It just takes trust and that takes communication on both sides.
The politician sees only the "big picture" and their objective. The career managers focus on their piece of the whole, like the management theory story of the five blind men and the elephant. It would really help if politicians would appoint someone with some practical knowledge of an agency instead of some crony of theirs, a noted business person, or an ex-military type. Having worked in the Defense Department, I suspect a former supply sergeant would make a far better SecDef than a general...