CPUs are normally mounted using silver conductive compound which is much less fussy about film thickness than straight silicone which is non-conductive and relies on a very thin, gap-filling application to do its job. AFAIK all the cpu manufacturers recommend/require it (silver).
That doesn't mean you put it (silver) on by the spoonful though. A thin wipe all over the CPU cover is enough to give a decent thermal connection to the heatsink (better than silicone).
Shorting out pins is greatly exaggerated. It's like a grease film. If you couldn't apply a thin film of that locally without getting it all over the pins you wouldn't be here.
Personally, if the original heatsink connection hasn't been broken, I'd leave it alone. It's most unlikely that you'll improve it. Cleaning out the crud that gathers around the fan and heatsink though with a vacuum cleaner is well worth doing from time to time, especially if you do any intensive processing (such as video editing). If you run a background cpu temperature-checker before and after clearing out the dirt you'll certainly notice a difference.