Cool idea! Some thoughts:
You have a lot of blasty powers that don't seem especially techy. I was envisioning more things along the lines of Remake and Rebuild or Seize the Machine. I'm not sure what you're going for with some of the witchfire powers. Is it just telekinesis type stuff channeled through a physical medium of "technology"? Like, telekinesis that only works if someone is wearing a wrist watch or carrying a gun? Just a nitpick there though. Let's look at specific powers.
Flesh Is Weak: This seems like a pretty reasonable primaris. It's roughly on par with other witchfire primaris powers, though the range could probably stand to be boosted to 24". No big deal there. WC2 for a power that feels possibly a little weaker than things like Smite feels off though. Why 2
WC? If you shoot it at an
MC, the
MC will probably ignore a couple of hits with its armor, and if you use it against lightly armored stuff, you usually don't need flesh bane. It still has a weird niche against things like grotesques though, and it isn't bad in general.
Break Reality: This one feels weird in a couple ways. If I'm not mistake, similar powers such as Phantasmancy's Mind Fog and the
WS/
BS dark angels power tend to be WC2. On the other hand, your version only works if the enemy fails a leadership test. Considering a guardsmen (let alone a marine or anything Ld9) is more likely to pass his test than not, that makes this power a lot less useful. You might throw that extra
WC die you have lying around at it, but it's more likely to fail than not against the vast majority of targets.
distort function: This just seems like a way better version of the previous power. Sure, it doesn't really help in melee, but it's a way more reliable method of limiting enemy firepower that also makes them unable to use flamers or blast weapons. I feel like this one should definitely be WC2 as either of its effects (restricting shooting or restricting movement) would be pretty impressive WC1 powers by themselves.
Omnissiah's Hammer: No mechanical complaints. I'm just not a fan of this whole techno-telekinesis thing that this seems to represent.
Techno Hymn: Cool. I like it. That's pretty darn good with a 12" range though. Also, using mastercrafted on an entire unit gets wonky because you'd have to roll every multi-shot model individually. How about a 6" aura or single-unit blessing of rerolling to-hit rolls of 1? It would have the benefit of being fewer warp charges than prescience while also potentially helping out far more units. My biggest concern is a psyker with this rule standing in the center of a carefully laid out gunline and basically giving an entire shooty army rerolls on their to-hit rolls for a single warp charge.
Remake and Rebuild: This one feels *very* powerful to me, but probably not WC3 powerful. It's like a more flexible Endurance that swaps Eternal Warrior for the ability to potentially heal wounvs at the end of the turn and make vehicles harder to damage. Again, seems rather powerful, but it's probably fine as is.
Seize the Machine: This is the first sort of effect that came to mind when you brought up the premise.

Is the immobilised effect permanent or just a one-turn thing? Permanent seems a bit too much, especially with a 24" range and especially against walkers. This would also let you make superheavy walkers pretty ineffective (for their points) by just lobbing some warp charges at it. Cool idea though!
I'd kind of like to see a power similar to that necron character's special rule that lets you shoot the enemy's vehicles at their own units during your psychic phase.