Reading between the lines, it doesn't actually look like this is ideological resistance. What they're actually complaining about is that their expert opinion isn't being considered:

Some department staff said they feel as if Blinken and his team are uninterested in their own experts’ advice as they focus on supporting Israel’s expanding operation in Gaza, where the Palestinian militant group Hamas is based.

This suggests that people who actually have a clue realize that Gaza operation is going to be a debacle, and they're actively distancing themselves from it.