So for some time we could not (or thought so) remove a VM from a job using the Remove-VBRObject and this is correct. It would just exclude the VM from the job, which isn't really removing the VM. I can't believe I didn't think of this earlier, by .Delete() works. So what we can do is the following:
($Job.GetObjectsInJob() | ?{$_.name -eq "Name of VM").Delete()
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