Greetings!
While we typically try to avoid making changes that can affect legitimate PvP interactions including players engaging in combat with faction-specific NPCs, this particular issue is noteworthy because of some under-the-hood changes we made some time ago to how the Rallying Cry of the Dragonslayer buff is applied in both Stormwind and Orgrimmar to improve server performance.
Without getting too deep into the nuts and bolts of what we changed, the important thing to be aware of is that being able to sap Overlord Runthak, Major Mattingly, or Field Marshal Afrasiabi during their event dialogue to prevent this buff from going out was not actually possible in original World of Warcraft. Sometime very soon we will be applying a hotfix that will more accurately reflect the correct behavior from original WoW.
These NPCs will still be able to sapped and otherwise crowd-controlled as before, but following this hotfix these effects should no longer prevent the event from playing out and the buff from being applied. Please note that the opposing faction can still attack and kill these NPCs after the quest is turned in but before the dialogue completes and this will interrupt the buff going out. This behavior is correct and has been preserved.
Thank you for the reports about this!