I've used the Intel RAID option on my Z77 EX 4 board, and other Intel chipset boards for a while now without any problems. I'm not sure what is happening in your case, but it should work fine.
First some info for you. When setting the SATA mode to RAID, all the Intel SATA ports are in RAID mode, which is not the same as AMD SATA chipsets. But, that does not matter, because any single, non-RAID volume drives, like your 840 OS drive, are treated as if in AHCI mode. So for any single drives on Intel SATA chipsets, RAID = AHCI. I don't get what you mean by it is forced to load in AHCI, that is not true. You can have six, non-RAID volume drives connected to the Intel SATA ports, with the SATA mode set to RAID, and those six drives will all work fine and are simply really in AHCI mode. TRIM still works fine for SSDs in that situation and always has in Windows 7, besides the new TRIM in RAID 0 for SSD RAID volumes, with our chipsets.
Clearing the CMOS does not clear the RAID configuration data on the drives, that data is stored on the drives. When you clear CMOS, you must reset the SATA mode to RAID of course, among other settings. The first time you boot after clearing the CMOS, you are not in RAID mode of course, and pressing Ctrl-I at that point, if it even works, will cause weird results.
On the first boot after a CMOS clear, just start the UEFI, which you should be forced to anyway, and reset to RAID and any other settings you use. Save and exit, which will then be your first start in RAID mode. If you have Fast Boot enabled, that can skip the RAID Option ROM from being displayed, and may not leave enough time for the HDDs to start up. Set Fast Boot to Disabled, IMO it causes problems with fast OS drives like your 840 Pro, and your boot will be fast anyway. HDDs take a while to start up, and they cannot keep up with your 840.
You can use the IRST UI that is available in Windows, listed in Control Panel, or from the IRST Task Bar Icon list. The IRST UI is delayed start in Windows, but you can start it any time.
What are you using to view your RAID 0 volume, the Ctrl-I interface, or the Windows UI? Even if you booted in AHCI mode, the RAID data on the HDDs should not be compromised, but the RAID 0 volume would not work of course. I don't know what is happening in your case, but you should not be loosing your RAID 0 volume due to a CMOS clear.