In Dominions, you normally get what you deserve:
" ... a big battle in an enemy capital. In one square, I had my prophet (a hero with nice gear and all), my main thug (Son of Steel with some nice gear) and one antlered shaman. ... my two most valued commanders ..."
This begs for punishment - and usually the RNG finds the most annoying way to hand it out, as you just noticed 
- you're storming a castle: expect lots of slingshots, arrows or even ballista shots from the defending towers. Any missile landing in the commanders' square would have little choice but to hit them - with 3 size2 units all slots are filled.
- any area effect spell would be guaranteed to effect all of them. Thats true for berserkers, but also for some bolt spells (Fireball etc).
- any melee attack (flyers etc) into the square would be guaranteed to target one of your valuable commanders as well
- obviously, you hadn't given them even ONE lousy bodyguard. While 1 soldier wouldn't help much if the quickened commander charges into enemy ranks, they would keep the commanders from bunching up too much.
- there are not many N2 battle spells. Do not let a N2 mage sit in the back of an army without explicit orders what to do. His first spell should be "eagle eyes", btw. .. "berserkers" is only prec0 and range 1 .. therefore can only hit the neighbouring squares .. or the caster himself.
Maybe "berserkers" should be altered to have range of 2-3 to make it 'easier' for spellcasters not to accidently hit themselves when they try to boost their neighbouring soldiers battle morale