I disagree. There's no reason such mitigations (not sure what exactly you're referring to) can't be implemented by the monitor process (ukvm in the Solo5/ukvm model).
I'd also argue that a normal kernel does not do any integrity checks on the code running in a user process, so the model is exactly the same.
> Even worse, the attacker could use it as leverage to infect other unikernel based instances of the app to gain some permanence against restarts by simply reinfecting when an instance goes down.
For that they'd need to break out of the virtual machine and into the hypervisor / monitor. Which is by no means impossible, but with careful design of unikernel-specific monitors can be much reduced. Of course, I'm by no means suggesting you should back your unikernels with a monitor along the lines of QEMU :-)