Flavor wise, shouldn't Sith Holocron be only Villain Blue Upgrades?

(Also, it would cut back some of it's power 'Force Throw' and 'Mind Probe' and whatever the new set brings)

There is a precedent for Sith Holocrons to grant force powers to non-force sensitive people.

There is a precedent for Sith Holocrons to grant force powers to non-force sensitive people.

I think the point wasn't for it to only grant powers to blue people, but only grant Villain powers and not Neutral powers.

Which I don't think would be appropriate. Mind Probe seems more like a Dark Side power to me, I was really surprised it was Neutral. Besides, evil Force users have been shown utilizing variations of telekinetic powers (which Force Throw represents) and full on defensive powers (like Vader absorbing Solo's blaster bolts), so it's not like those are Light Side exclusive. To be honest, neither are traditionally 'evil' powers exclusive to Dark Side practitioners. Luke goes around choking Jabba's guards and I'd argue Qui-Gon uses full on mind control when dealing with Boss Nass that goes beyond a simple distraction mind-trick.

Years of gaming media that named and categorized Force abilities have polarized them into clear-cut Good-Evil sets, but it is clear from the movies that it was meant to be a bit more esoteric than a binary 'morality' system of a cRPG.