Most larger heatsink/fan combos have a backplate for your motherboard. This relieves any problems with damaging the board, as it sandwiches the board between the heatsink and the backplate, spreading the weight.
In the end, in the long run, AIO water coolers are more efficient in cooling, in space utilization, and stress on the motherboard. The hassle factor is a little higher, but worth it in my opinion.
That's an old bugaboo, long since put to rest by the AIO coolers. They come pre-assembled and pre-filled, so it is desperately difficult to get one to leak.