There are various architectural reasons that the prime client must be run on a physical system. Any run where the prime client was run within a VM would be considered non-complaint as well as it would not be comparable to other VMmark 2 results. It might however work if you were trying to debug an environment but I wouldn't recommend it.
I can't think of anything in the benchmark that would stop this but due to it not having been tested, I can't say for sure. Due to the additional role/load you might run into unexpected performance issues.
I've run prime on a VM. But I think Joshua's comment about the compliancy and impact are reasons not to. In my deployment Prime and all of the clients are VMs. I had to bump up their memory and such to remove performance issues I saw with them. And another thing, if they are hitting the array hard, they induce enough load to skew the results of the tiles.
