Sorry that I misunderstood what you were originally describing. The only way you run the risk of destroying/corrupting your VMs is if you selected the RAID5 logical volume by mistake for installing ESXi onto vs. the SD mirror cards. Otherwise the installer does not touch the other volumes.
You'd run the same risk if you were installing ESXi 5 on a server with FC attached storage; the installer would see all the SAN volumes and present them as possible locations to perform the install. It's just a matter of selecting the correct location to install the ESXi image.