I assume all these Unikernels Are targeting the Cloud and Server Usage? Which is perfectly fine for GPL.
"Consult a lawyer" would be the best answer I could give here. The applications we're actually targeting are open source servers of various kinds (think memcached, apache, etc.) so it's not an issue we need to consider ourselves as the licenses will be compatible.
No one really knows if the Linux "userspace is not covered by GPL" applies if you link an application to the kernel. Or if you then apply link time optimisation.
In the cloud no one can hear you violate the GPL.
This is why AGPL exists. I think it is agreed that deploying your app to the cloud is not distribution and doesn’t run foul of plain GPL.
In the cloud you usually don't distribute binaries, so you don't have to distribute sources either.