Pretty much this. The Alliance draenei were under the command of the Alliance commander on Draenor.
Blizzard is really bad in telling a story like this; they want to make these draenei look like villains, but they're apparently trying to subjugate the same guy who lead the Iron Horde on an extermination spree on the AU Draenor draenei and then attempted to conquer Azeroth too; only once he got beaten did he get chained down by Gul'dan and once we as players handle Archimonde, he pretends like it is his victory. Bottom line is that even if Y'rel is doing this, it basically equals "getting back at the AU Draenor orcs for what they've done/attempted to do".
Every time some Horde race is being portrayed as a victim, the ones attacking them are those this Horde race attacked in the past. Blizzard is using this formula throughout Warcraft's history and keeps recycling it. AU Grom being alive and not getting punished for the Iron Horde is a huge mistake, while killing Durotan and turning Y'rel into a potential villain is a continuation of this wrong twist. Durotan and Y'rel were some of the best characters WoD gave us.