Right now inorganic status eliminates too many possible interactions. It cuts out a whole huge potentially interesting section of the game.
I suggest that, instead of being a sweeping "unaffected by spells or skills", you have spells or skills specify whether they affect only organic units or not, based on whether it makes sense. So for example, the Necromancer's Kill spell would say, "Kill enemy organic unit." While the Geomancer's Entomb spell would keep the current wording, meaning it effects both organic and inorganic units.
Here's my opinion on which abilities should be changed so they affect inorganic units too:
Black Mages
Witch's Curse, which should also affect inorganic units, because even machine's can be cursed to malfunction.
Clergy
It would make sense if holy magic only cared about living things, ie, things with souls, therefore all Clergy abilities should affect only organic units. However, if that wasn't a rule, Acolyte's Shield, Archangel's Aegis, Shield Maiden's Protect, should work on inorganic units because even inorganic units can be protected.
Commanders
Captain's Coordinate, because even inorganic units are being commanded. The rest, should remain as is, because they're all psychological in nature.
Nature
Geomancer's Entomb, because even machines can be buried in rock. It is unclear how Shaman's Guardian works, so that could go either way. I would encourage making it affect inorganics, just so that more abilities mattered for inorganics.
Siege
Ballista's Push
Soldier's
Axeman's abilities, because if his axe can chop armor it can definitely chop machines.
Footman's Interference, because you can interfere with the movement of machines too.
Warrior's Rampage
White Mages
Abjurer's abilities, because even machines can be teleported or protected.
Wizard's Switch Places
This change would also allow creation of new spells or skills that affect inorganics in a way that makes sense... Disable, Reprogram, Inflame, Shatter, Repair, Move, etc.
It would make more sense for some powers to effect inorganic units, but it would make it more difficult to know how and which will effect inorganics and it would be a lot of work to make all those changes.
The game has a steep enough learning curve as it is; I can't imagine complicating the inorganic categorization as being beneficial to the game.
Inorganics are a great function and are needed to balance the rock-paper-scissor part of the game. Perhaps inorganics should actually be more simple, but I'm not sure how to elaborate on that.
Anyhow, The problem I think you might be refering to stems from units creating unwinnable scenarios like a magus, angel, spamming too many summons or maybe a heretic. Like an inorganic, it spoils the fun if your super piece gets hosed so quickly or if your opponent has an unkillable piece. The game is really balanced, but perhaps more pieces like the geomancer should exist, to help keep the game simple but fuel the rock-paper-scisssor.