I agree that you shouldnt be able to dodge or counterattack when prone, ive put a bug in for it. I'm fine with counterattacking when casting, i think its less confusing than wondering why your unit didnt counterattack in some situations.
That's fair enough, I agree that would be confusing.
Another idea, resurrected from discussion in 425343:
A counterattack could interrupt the spell, being clearly indicated by "spell interrupted" message. Then mages have a choice: battlemages may carry a dagger/sword to defend themselves in melee at the expense of their spells, while archmages skip the blade to focus their attention entirely on their spells, and give up the ablility to dish out free damage in melee. The blade initiative bonus adds even more choices to the mix.
On the other hand, fast attackers who spot a caster with a blade can try to force a counterattack to interrupt the spell.