It is a damn shame our federal government is this incompetent. It's only be three months and we are destabilized.
We are vulnerable.
Honestly, the Federal government is running more or less as well as it ever does. The bulk of the work at the various Departments and Agencies is done by career employees that are not and cannot (easily) be removed by the current administration.
The top of the 'food chain' is usually an appointee from the administration. However, these appointees are relatively short term and even when they aren't as grossly incompetent as many of Trump's appointees have been, they are rarely qualified or have the background to understand what they're truly in for or to be effective at it. As a result, 99% of things remain in the hands of the career employees. Appointees can obviously set the tone from the top to an extent and push certain changes but there is definitely a limit to what they can accomplish without truly understanding the agency they're now 'leading'.
The biggest drivers for change come with the annual President's budget that more or less says "Here's how much money we're going to spend and what we're going to spend it on". This is a big process with input from the various agencies and OMB and the Administration. It does provide a lot of guidance for what each agency is supposed to do. What programs receive funding. Which lose funding. Which stay the course. This budget is submitted to and approved by Congress. In theory, with a Republican President and a Republican majority in Congress they should be able to pass this in time, without continuing resolutions (as we've dealt with for quite a while now). We'll see...
All that said, currently the agencies are more or less running as they were 3 months ago and the new fiscal year doesn't start until October 1 for any sweeping changes to truly be possible.
It's pretty hard to stop a bureaucracy of tens (or hundreds) of thousands of moving parts.