I moved your question to it's own thread. It easier to find for other users that way.
Yes you can certainly throttle SMVI back to a single backup at a time to reduce the impact on the environment. You may also want to consider not using the VMware snapshot as part of the backup, that would eliminate the load all together. The VMware snaps do flush out the write buffers on the VM but don't offer a significantly higher level of consistency over just the NetApp Snapshots. Alternatively you may create a seperate backup job for just the VMs you want the VMware snapshot on and then a general one that does not use the Vmware snaps.
Keith