We use nfs, and use netapps mbralign tool from a linux non-ESX host. You could even use a VM that mounts the same storage, to align vmdk files (while vms are off), but latest mbralign doesn't work. The one we have that works is mbralign version 1.40090416. the newly released toolkit 2.0 has a new mbralign and no mbrscan. the new mbralign doesn't have a version number and works to check vmdk files (via --scan flag), but when attempting to align it throws an error about 'cannot find mbralign.pl at line 1667'. It appears broken.
This post is quite old, and from what I can see this is still an issue. I tried the mbralign tool from VSC 2.1.1 (most recent version as of this date) on a .vmdk on ESX 4.1 and it was unable to realign it. It did the scan the whole datastore thing.
I did download the 5.1 version and it worked like a charm (no corruption), but I still can perform scans using version 5.2.
I've not been able to locate a new, fixed version of mbralign. Does anyone know of one out there?