If the enemy with mistform is a lone commander, you could put a couple of mages up front with instructions to cast some high-precision armor-negating spell several times, such as Lightning, Drain Life, Incinerate, Frozen Heart, or Shatter, depending on what you can cast and what the enemy is vulnerable to. Or give somebody an item that casts spells, such as a phoenix rod or spirit helmet.
If many enemies have mistform... yes, Flaming Arrows, Falling Fires, uhh that astral-and-death spell that makes a shower of glowy things, Earthquake, maybe Foul Vapors, various other large-area attacks that pierce or negate armor... really your question is more about how to hurt an enemy a lot in spite of armor, because once you've hit somebody with mistform hard enough to hurt them a lot in spite of their armor, they lose their mistform. So, learn how to hurt a well-armored enemy a lot (there are a thousand ways, and they vary according to what other vulnerabilities the enemy has) and just do that.
Or you could just cast lots of large-area protective spells on your own army to give most or all of them more armor, maybe regeneration, maybe even mistform. Then they might live long enough to batter through the enemy's magical protection.
Re: Tips for fighting misform units
Hybrid Mode
