It's probably better than the closest antipodal alternative, i.e., mass turnover of all bureaucrats for each election.

I think the problems some people have with the deep state gets lost due to how they talk about the deep state. Their problems are more akin to a deep state so entrenched in power that is becomes corrupted and undermines better governance. The way people who believe that tend to talk about it is "deep state bad".

The deep state issue is probably a natural phenomenon and unavoidable. However, it can probably be mitigated by using a better system of selecting for the deep state and its most relevant components.