A few years ago someone trying to spin container technology did a lot of damage to other attempts at unikernels with marketing dogma, not reality. Claims of non-debugability and other FUD. It's long been standard operating procedure to trace and debug systems from outside the system's view. This is how people do bringup of new chips as well as OS ports. On hardware there is usually a dedicated debug and trace facility as part of the CPU or board support package or a firmware monitor. In a virtualized environment like a unikernel this is way easier because you can run code above the guest's ring 0 supervisor privilege against its RAM/pagetable root. Modern systems like POWER even allow debugging from the BMC, with a plan to allow full gdb sessions over that out of band interface https://github.com/open-power/pdbg.
There's nothing implicitly wrong with unikernels, or other systems software ideas like microkernels, just because they are less popular technology at the moment. I'd encourage people to continue exploring this space.