I don't think high threat would be unfair to raiders considering we have omen as well as mind flay. It would make a more involved rotation if we tried to maximise spikes without pulling threat.
But Mind Spike isn't a rotational spell; that's presumably the main reason it's received the adjustments it has. It's not intended to replace Mind Flay in the PvE or PvP rotation.
In PvE, Mind Spike is for burn targets and adds that need to die fast (10 seconds and under). In such a limited window of time, Omen barely even becomes a consideration. If Mind Spike had a high threat component, its use could cause serious problem for tanks trying to pick up said adds. Shadow priests would be forced to sit there and evaluate whether or not they can Mind Spike a target that needs to die immediately...that isn't just counter intuitive, it's totally not fun.
Good shadow priests would learn the nuances of these situations and be able to manage the high threat/kill the aggro'd target before it reaches them, but more often, raid leaders and tanks would simply say "Yeah, don't use that spell". Every class has certain abilities restricted at certain times (i.e. "don't AoE here"), but burning adds down fast is what Mind Spike is designed for in PvE.
Your concerns about Mind Spike in PvP are entirely legitimate, but I don't agree that the solution is to put high threat back on the spell. It's probably safe to say Blizzard feels the same way, as they have moved on from that idea.
What I said about high threat Mind Spike being counter intuitive (and not fun) in PvE applies to DoT removing Mind Spike in PvP. It's a big problem, but the solution is not to change the spell in such a way that it makes life difficult for our PvE counterparts. I'd rather see a solution that satisfies both the PvE and PvP sides of the shadow priest community.
Dark Archangel should let us spam Mind Spike without it removing our dots.
This is a cool idea, and tying our controlled burst to a cooldown feels fine from a balance standpoint. I'd still like us to have our reliable root w/ DoT pressure independent of that, however (same goes for when we're locked out of shadow).
Edit: Grammar fix