From Page 127 of the
BRB:
Allies of Convenience wrote:Units from the same army that are Allies of Convenience treat each other as 'enemy units' that cannot be charges, shot, attacked in close combat, or targeted with psychic powers. This means, for example, that:
...
-- Are affected by attacks, special rules, or abilities used by Allies of Convenience that affect 'enemy' units within a certain range or area of effect.
So the way that I read this in terms of the scenario given is that as long as the Target Unit was an 'enemy unit' (as opposed to a unit that belongs to the Allies of Convenience), then it was OK to make that attack in spite of it hitting your Allies of Convenience.