Just a thought - if the backplate screw heads are long enough, did you think about adding some additional nylon washers/spacers between the backplate and motheroboard at each screw location? My cooler (Thermalright H-02) came with them so I had no issues with the long backside pins.
If you're US based, Lowes, Home Depot, or Radio Shack would be good places to find them. At Lowes or Home Depot they'll be located in the same aisle as nails and screws in the speciality items drawers. You may also try the folks at www.frozencpu.com and see if they offer spacers. I can't believe you'd be the first to have run into this issue.
Good luck. And post back if you find a workable solution. Thanks.
I tried 2mm washers which are for S1366 mounting, already. But the board looks still pretty uneven with it. And there would be much more force on a smaller area with them.
The Backplate from Mugen3 would be a lot better.
But i think even with the Mugen3 backplate there would be some amount of pressure of the pins which could weaken the soldering.