I'm not arguing that the Tories do want things to change (honestly, I think the status quo suits them just fine), but even if they did, even with a huge Commons majority, they can't govern the country without the civil service.

I the people who staff their Ministerial departments, who are actually responsible for enacting all of their policies and training the next generation of civil servants: if those people don't want to cooperate with the government, if they have their own agenda, then there's not much that elected representatives can do about it. The infrastructure they need to implement their agenda would be literally working against them. It's like if the road suddenly grew spikes under your tires while you were driving.