> Civil service rules are quite troubling. I can see the idea that it shouldn't be easy to make everything political, but the problem is that this goes only one way.
No, it doesn't, there are rules protecting against patronage hires to civil service positions; they aren't perfect, but the protections aren't one sided.
> If the president's predecessor hired a few million hostile partisans
Not gonna happen, since it would take not only an unprecedented politicization of hiring but also a President getting to fill half the current federal workforce.
> Is he just supposed to continue down that path, hiring tens of millions of his own partisans in order to win back control?
Uh, no, the President is not supposed to have partisan control of the federal civil service workforce.
> There needs to be a reasonable way to toss out the partisan troublemakers who are undermining the will of the voters.
If they aren't doing their legal duty competently, federal civil service workers can be fired for cause. Not being a partisan of the President, isn't cause, and that's a feature not a bug.
> Another troubling rule is that layoffs must be done according to seniority and veteran status, not performance.
I don't see that as troubling at all.
> The only reliable way to eliminate low-performing employees is to eliminate everybody in a given agency.
No, the reliable way is to set performance standards at the appropriate floor and then fire people who don't meet them for cause; civil service rules do allow for performance standards and do allow firing people who don't meet them. You know the practice of PIPs in private employment? That's directly modelled on what is required for performance-based termination in civil service employment.
Layoffs fill a different purpose.