Gameplay value should trump realism (otherwise the bases should be at least a few hours of walking from each other, now shouldn't they?), and the added management of having to baby-sit your trolls (or cavalry, for that matter) is certainly something that isn't desireable. I don't think making them chase after the most vulnerable units is absolutely necessary, just make it so that they won't run towards the ones they're vulnerabe to.
Yeah along with realism I think that is a bit over the edge yet it still needs to be realistic. This goes along with the troll thing but, what if say 15 archers shot at a troll and since its hide is so thick the arrows would stick out of him like in the scene of LOTR ROTK where the Mumakil got all shot in the legs.