Small factions spamming full stacks is not much a problem for any empire with good steady economy. I remember that in my Roman campaign Lusos were reduced to two settlements, but they had like 3 full stacks of troops. Eventually I've killed them all, but at that point I had tons of money and could support numerous full stacks on all fronts.
It can however be a huge problem for economically struggling factions, like Pahlava, Hayasdan etc. I think that making AI assistance script work in some kind of dynamic way could solve that, but I'm not sure it is possible, and even if it is possible, EB team priorities lie elsewhere.
Bookmarks