As you indicated, VSC will manage the ESXi hosts for settings and paths instead of the Host Utilities Kit. Unfortunately MBRalign needs a service console. Are you useing FC, ISCSI or NFS for connectivity to the NetApp? We are working on a new tool that will allow alignments on ESXi, until then you will have to either align the VMs with a ESX server before moving them to ESXi or perhaps look at a 3rd party alignment tool that aligns from inside the VM.
Keith