If a new gun is fired even one time the bloom is off the rose, so limited shooting will not have much effect on value.
What lowers value is getting the finish worn more or it developing mechanical problems, something the later Colt's weren't prone to.
The Peacekeeper is the same quality internally as the Trooper Mark V. It was just the outside that was changed to the unpolished parkerized finish. The Peacekeeper is every bit as tough and durable as the polished Trooper Mark V.
Like all Colt's the Peacekeeper will continue to increase in value, and it's possible they'll go up faster due to the lower production.
Bottom line, shoot your Colt and enjoy it. Since it's not new in the box it will be many, many years before it ever becomes anything like a collector's gun, so you might as well have fun with it.