After doing some digging I think I am in a position to answer my own question.
There are two conflicting bits of information on the Intel site...
From the Intel SSD Toobox software user guide, page 11 it says...
"Intel Rapid Storage Technology driver V9.6 supports the Windows 7 Trim command, but for Non-Raid configurations only. In these configurations Intel SSD Optimiser is not required to enable trim"
This wording kind of suggests that any hint of raid borks trim support, I guess including the event that Sata set to raid mode in bios but only hdds in the array. This paragraph in the user guide is not exactly clear though, as you could equally read it as saying that you are okay as long as the ssd is not part of an array.
However, a separate bit in the intel site says...
"Intel® Rapid Storage Technology 9.6 supports TRIM in AHCI mode and in RAID mode for drives that are not part of a RAID volume."
This seems much more emphatic about it and answers my question, though it would be nice if they could make their own user guide pdf as clear as this.
So as long as your SSD is recognised by the BIOS when you initially install windows with raid enabled in bios then it should work ok and have trim support as standard, as long as you don't put the SSD in an array.