I cant really get what you are willing to achieve.
If you want to delete raid 0 here is the solution... but you will loose data from those 2 drives... since it works that way!
If you cloned the matrix, you have that data on that cloned HDD.
1 - you need to unplug both raid drives and check that this cloned one will boot correctly
2 - unplug that cloned drive and plug the raid drives
3 - go into Matrix Manager (Ctrl+I while RAID screen shows up during post)
4 - delete the raid volume.
5 - done
More hints:
Intel Raid Configuration Site