Bug with Shapechanging commanders

[Ygorl]

Suspension of disbelief:
Some folks are more inspiring, efficient, and capable than others (higher leadership) and can therefore command the attention and fealty of a larger group of troops.
Once said troops have already agreed to follow a particular leader, though, they're not going to run off just because the leader happens to turn into a wolf. As far as the random events, remember these people are motivated by religious zeal to enlist. This religious zeal temporarily makes the priest a more impressive figure in their eyes; once they're in the army, though, things don't look quite so rosy. If you give them furlough and then ask them to re-deploy under the same commander, some of them will resist.
(you can get a similar effect with the spell that summons a small undead army into a distant province, but I leave the justification to the reader... )