There's a greater chance of damaging your system from an improperly mounted HSF than there is from breaking your motherboard because of the HSF's weight and how it's distributed.
HSFs breaking motherboards is a myth, in my opinion. Consider this: The HSF manufacturers (Scythe, in this particular case) stand to lose their entire business if any of their designs and products could cause a catastrophic motherboard breakage from their products' sheer weight. Think of all the lawsuits/RMAs/bad publicity that would result if this was actually something that happened on a regular basis.
The real key is in the installation. Ensure basic compatibility (will it fit in your case? Will the HSF impact other parts of the motherboard, such as certain VRMs or capacitors near the CPU socket), then follow the instructions (RTFM, always!) when installing the component.
Your installer is probably just the cautious type. I don't really understand his reluctance, especially given his extensive experience as you cited.
I've got the same motherboard, and in various iterations it's had a Thermalright SI-128 + 120mm fan (heavy), a Thermalright Ultra 120 + 120mm fan (not as hefty, but still heavy), and presently a Thermaltake Big Typhoon (very top heavy). I've never been worried about any of these big coolers destroying the motherboard.
Hope this helps (if only to assuage your concerns).