I think I managed to resurrect the guest machine. Since the errors that I was receiveing were write errors and the ESX box was having difficulty replaying the journal, I figured that everything would be OK if I could get the data onto writable drives. I copied the 3 LUNs back to my Linux LVM system, and I can now see the missing machines in datastore viewer. I'm copying out the vmdk files to an external USB before turning it on to make sure that I have a copy before anything else gets corrupted.
I put some details on the FreeNAS forums in case anyone Google stumbles across this at some time later: http://forums.freenas.org/showthread.php?4169-iSCSI-Write-Error-causing-VMFS-corruption.