Honestly, I wouldn't complain at all if they were disabled in PvP. I'd probably pick whatever looks most interesting (either lore/aesthetic or just the ability itself). 1% DPS in raids or M+ is probably not going to make any difference at my level of raiding/M+.
But since they work in PvP, I'm just going to pick the best one for PvP on every character (let's face it, for most classes there will be a clear winner, for some maybe two will be decent). For arenas I'm pretty sure even at my level (2k at most) it's going to make a big difference.
Imagine playing a Retribution Paladin in 2v2, and picking Kyrian. You get an awesome ability - Judgment, except on a 1 minute cooldown! Meanwhile, the enemy paladin just buffed their healer for +20% healing done and taken.
Or any kind of Druid picking Venthyr, with Ravenous Frenzy. Nothing is better than having a major cooldown entirely counterable with any 1.5s CC. You'll get shut down any time the enemy wants, and maybe also get a nuke to your face. Fun!
In theory, they could balance the covenant abilities in PvP specifically, so that everything is viable. In practice are they really going to make sure that all 4 covenants are viable on every spec, when they can't even make every spec viable?