The reason you want to hold a cpu from the sides is to keep from bending the pins on the bottom and to keep the natural oils of your skin off the CPU heat spreader. The oils will interfere with the thermal paste resulting in less then optimal cooling performance. The oil from your skin won't damage the gold cpu pin or contacts but it's just good practice to not touch it.
If you can't hold a CPU from the sides place it on your palm heatspreader side down. Then after you get it into the socket wipe off the surface with rubbing alcohol before applying thermal paste. If your CPU is working fine now, there won't be any damage in the future as a result of your touching the top and bottom.