Just off the top of my head, here is a list of things that the Chancellor can do without violating the Charter. If you are in good enough standing with the Chancellor or are willing to pay his price, all of these may be available to you. If you have enough standing with the Chancellor to actually make him violate the Charter, there are no limits to what you can do.

1) Have your enemies' armies disbanded.
2) Have your enemies' armies march in the wrong direction, slowing their progress.
3) Have your enemies' armies march into battle against a much stronger foe.
4) Make sure you enemies do not receive reinforcements for their armies or only very poor quality reinforcements.
5) Prevent your enemies from having any of their build queues completed.
6) Have you enemies' avatars stuck in places where they can obtain bad traits.
7) If the enemy forgets to give instructions on the tax level of his settlements, the Chancellor can jack up the tax rate, disband some of the garrison, and cause the settlement to revolt.
8) Have your enemies with low piety march near Inquisitors.
9) Have your enemies march near enemy assassins.

I am sure I can come up with many, many more, but I think you get my point.