To be fair, we are seeing this scenario from the Horde's perspective. For the AU Mag'har Orcs, the AU Draenei are their oppressor, so it's not strange that they would appear as some sort of Well-Intentioned-Extremist or simply Zealous to be worried about. If we get a scenario from the Alliance's perspective, I'm sure those AU Draenor could look a bit less villainous.
For example, if we get a campaign for the Alliance to recruit those Lightbound Draenei (I don't think we ever will, though), it could go like this:
- The Alliance arrived at AU Draenor's Shattrah. We got a warm welcome from the Lightbound, who still remembered who we are and what we did to help them.
- Yrel told us that after the defeat of Archimonde, the Naaru helped them to clean up the rest of the Legion. Even the Orcs cooperated. They worked hard to cure the planet and protect it from being corrupted again. Together, they formed the Lightbound force, an united front of both Orcs and Draeneis, and have been working to restore AU Draenor. For the first time in many years, peace and unity seem to be close.
- Yet, a group of Orcs refused to change. They clung to their savage, barbaric traditions and don't want to be blessed / empowered by the Light, even though this means they are risking themselves (and the planet) being corrupted again by either the Legion or the threat of Void. They also obstruct the work of the Lightbound.
- The Lightbound approached and tried to convince the Orcs to no avail. Recently, the relationship between them have soured, and there have been skirmishes here and there. This doesn't bode well for the planet and the peace they finally attained.
- "Heroes, would you lend us a hand to convince them? Here is one of our new Exarch, son of the Warchief himself, he will guide you and his force, just in case a fight breaks out"
There, from that perspective, while the story is more or less the same and the Lightbound would still be zealous of the Light from the Orcs' perspective, to us the Lightbound'd probably look a lot less antagonistic while Mag'har Orcs would seem like anti-vaxxers stubborn people who threatened the peace of AU Draenor and the planet. Thus, I don't think the current story in Beta is too out of character, especially given a long time has passed since the last time we saw them. Is convincing people to go your way by force evil? Well, maybe it is slightly so, but even we - the heroes - have been doing it many times in various quests. As long as it doesn't hurt us, we probably can let that fly.