How can I use NTFS and iSCSI and not corrupt my SAN?

Solution 1:

You can't do it with NTFS as isn't a cluster aware file system. MetaSAN and StorNEXT are cluster file systems that can be used with Windows, StorNext was OEM'd by Apple as XSAN.

I would suggest wikipedia for further reading

Solution 2:

NTFS just can't be accessed by more than one machine at the same time; even when you use Windows' Failover Clustering, only one node has real access to the volume at any given time, the other one is blocked from accessing it by the cluster subsystem.

Accessing the volume from one server and sharing it out is really your only option here.