Our exchange environment had been setup the same way, but was relatively easy to convert. You have two options if you can take the downtime and have some spare storage.
The easiest is to add a new VHD(X) to the VM and use the EMC to move the mailstores to the new drive. Handy if you have multiple mailstores as you only have to take one offline at a time to move them. If you have corrupted items etc... in the mailbox it can be a real pain in the backside.
The other is to use Disk2VHD to create VHD's of your attached iSCSI disk (obviously take all Exchange services down first). Take the iSCSI volume out and give the VHD the same drive letter and Exchange is none the wiser. This route takes the whole of exchange down, but depending on your SAN etc... can actually be quicker than moving mailstores with EMC.
As usual make sure you've got a good backup first