Mercenary mode was introduced because nobody wanted to play PvP on Horde side. Why? Because they kept losing and because Horde side is subpar when compared to free PvP trinket from humans. So no, I wouldn't say there's an imbalance in PvP, you just got hit by **** RNG.
You can enable mercenary mode here:
https://www.warmane.com/account/settings
Speaking from Horde side, every WSG that I get in is a premade gy farmfest and it's over before it starts. There's plenty of premades where I'm from.
Alliance also have more healers in BGs on average which realistically nets them more wins.