Although Dragon Pulse is the lowest "True DPS," the difference between it, and the other moves, isn't relative. The only way you're going to achieve the "True DPS" is if you're using your charge move each and every time you have enough energy; However, we know that it isn't always smart to do that because, for example, using it would be overkill.
As to your concerns of future player verse player combat, unfortunately, Dragon Pulse has the largest dodge window of all of Dragonite's charge moves. Thus, landing a hit will likely be more difficult.
All in all, it would be a much better attacker than a defender. But even with the worse move set, Dragonite is still a beast defender. Since this is your second one with perfect IVs, it is likely that candy isn't an issue. So if the only thing holding you back is stardust, I would go for broke, pump him (or her) up, and ball-out like a boss.
Good luck, Buddy.
