To reconfigure, the admin would simply reset it and start the system with "init=/something/else" as kernel parameter that booted to a normal userspace.
This is one of several major arguments made against unikernels in that famous Triton rant from a decade ago:
https://tritondatacenter.com/blog/unikernels-are-unfit-for-p...
Basically, even if your application _can_ run as the kernel, and it's desirable for it to run with kernel-level permissions, do you really want production to be a world without strace and iotop and the like?