I got this idea from a question by Ze German about whether you choose a target before rolling for the assault cannon. I've always played it as you do but that still leaves the problem of knowing which aliens to attack after the first target because you know what your score is and can't possibly miss.
Assault Cannon: Choose a target and roll the dice as you normally would. Any left over score after destroying the target gives you an additional attack. Choose a target as normal and roll again using one red dice for each unused score one the previous attack. Repeat this process until you either fail to destroy a target or destroy a target with no excess score left over.
Overall this makes the assault cannon less effective because you don't know which targets to go for after the first attack (the overall score averages exactly the same because a red dice averages a score of 1) but it can potentially score enough to wipe out any group of targets.
I've always felt that assault cannons are the least killy of all the heavy weapons. They're great for clearing a room full of gretchin, but in every other instance, the other heavy weapons are more likely to kill more enemies (since the AC has to overcome armor on every model you hit).
For this reason, I don't feel like it is problematic to let the AC choose its targets after rolling. That at least gives it some advantage vs. the missile launcher and plasma gun.
With your rule, would you be able to stack extra attacks on a single target, and roll X number of red dice to attack?
If so, the AC would be a brilliant way to take down a dreadnought (you first shoot at some grot, then assign all of your other dice to the dread- you could end up rolling four red to break its armor!).
Yea that's the idea. You could also play it so that you roll two red dice to start with but just to determine the number of red dice you use to attack with, makes it a lot more unpredictable and you wouldn't have to kill a gretchin first to take down a dread. If you ever need to roll more than six dice then it could jam. I'm not sure if I like these AC rules or not, Mortis' ones might be better, although there is an auto-cannon as well in the White Dwarf rules so both could be used.