There's the issue of food as well, I've never kept an army out of territory too long, but you'd need to account somehow for the fact that the spawned general is gonna be spending a lot of time out of supply range, so the bottomed out morale and tiny movement points mean the army would probably get crushed by Romani spamstacks.
If it's possible to make the general exempt from all of these things (morale bonuses, the teleportation thing you were talking about), then I guess there's some working space.

Also scripting events for the faction will mess up certain areas of the whole game badly unless lots of other things are scripted or hardcoded as well. For instance, sending a rogue Hannibal into Italy implies that the two factions are already at war. If they aren't, it might mean that either one could get crushed way too quickly from fighting too many fronts at once, when if they were at peace, the factions would progress more naturally.

I suppose it wouldn't bee too hard to arrange it so that the character only appears after certain conditions are met (most noteably war), but from that an innumerable amount of further problems come up.

To be honest, scripting characters like this removes the "what if" factor from the game; in order for everything to work smoothly you'll have to make set actions for every possibility, otherwise you'll end up with Hannibal in Northern Gaul or something ridiculous like that. at a guess it's too late to be able to edit the EB files to make it happen, you should have a go at EBII instead :)