Currently the only thing you can do with the AI is tell it to get out of your territory. The AI will come right back in the next turn, and it will happily do it every single turn. Not every time, but eventually, the AI decided that even though I told it to get out of my territory it would go through my territory to the other side, and settle. This wouldn't have been too bad an occurrence I guess, I had the audacity to play the game and not baby sit the swarm of pioneers telling them to get out of my territory for a few turns so it managed to get past the half way point in my territory. The only problem is, earlier in that game when I was killing a monster and one of their pioneers settled near my army, instead of booting me back just outside of their territory it sent me over a dozen tiles away, just outside my own territory.
There really need to be some established rules to the "Get out of my territory" option. It would be nice if there was at least a ten turn interval where reentering the territory would automatically declare war so the AI would not just come back and come back and come back until you had a turn auto-end. To that end, it would also be nice if one of the things that prevented the autoturn was any member of a faction you had not explicitly allied with being in your territory. It also would make a bit of sense if it was harder to travel in unfriendly terrain, the fact that the enemies Pioneers are just as fast in my territory as my own pioneers who would presumably have access to maps and be more freely able to utilize my roads is more than a little silly. That feature was quite useful in Civilization for ages, and it would help me keep from having to literally put a line of soldiers in every single square along the borders of my territory.
And the most frustrating part of this situation was, when Krax got to the other side of my territory and established a couple of altars he had enough mana to send endless waves of skeleton armies into my territory. I got practically nothing for killing them, they did ridiculous amounts of damage, and they didn't count as him causing trouble in my land even though I knew it was him. This tactic is silly both for the AI and the player, if I start seeing pioneers protected by summoned skeleton armies wandering through my land, I am pretty sure I wouldn't need someone to draw me a picture to gather that those units were his. I was hoping the diplomatic options would be considerably improved, and so far it seems like they could use some serious work. I know I could have just declared war on Krax and in theory walked over his towns as soon as he sent his armies to my cities and I broke them. However, that is hardly the point. I was producing pioneers quite regularly, expanding my borders as quickly as I could without sacrificing city growth, and Krax still managed to produce far more pioneers and force them across my territory to start expanding on the other side, as I had a higher military rating than he did so he didn't start a war. These are significant flaws in the AI in my opinion.
The easiest fix would be to have unallied AI units kick up a nag message, and extend some amount of time during which it was impossible for the AI to enter my territory without declaring war, perhaps depending on game speed. As I was playing on the Epic game speed, it was all the more frustrating to have to micromanage his waves of pioneers. It also wouldn't hurt if the unit in question was actively sent back to their own territory, this would be a boon to players when they were caught exploring on the far side of an enemy and got boxed in by new expansion. I have been shunted back into a tiny corner repeatedly in earlier Elemental versions, although I will admit that the one time I was sent out of the enemy territory it put me right outside my own, so that may not be an issue any longer. If that is the case, it would simply require making those rules apply to the AI.
TL;DR: AI being told to exit territory should effect a ban on them reentering without declaring war for a number of turns dependent on game speed, the AI should be sent back toward its own territory rather than being allowed to finish crossing yours instantly.