First, I also think the suggested "pay for passage" would be a nice addition and if easily doable it ought to be added. It would certainly spice up some extort... umm... friendly protection deals

. The key point would be that the AI can make effective use of it, though.
OTOH the "ROP rape" is not really an issue in a purely human vs. AI game provided the player has an either-or attitude towards this. The AI does not use it ever, and if the player feels it to be "against the spirit of the ROP" then he can simply choose not to use it and the issue never arises. OTOH if the player does use it, then it is like any other "cheat". Your game, your fun. Just like cheating in solitaire: the only one whom it matters is yourself. Neither the computer nor the cards won't care.
However, this is not the whole issue, because then there are people like me

who think that a ROP based blitz ought to be a viable option at least to civs of certain character but that using it should then not be a "cheat" but an available strategical option with its pros and cons adjusted with suitable offerings to the dreaded deity of Game Balance. The historical accuracy is IMHO not as important in this case as playability, enjoyment and game balance.
One way to try to solve this is to think about two human controlled civs playing against each other. If they have a ROP arrangement what would be the warning signs that a blitz is coming? If we can list very simple clues at what to watch perhaps the AI could be enhanced to notice the deceit? Of course, this would mean that you (and AI of course) should be able to cancel a ROP deal, and more to the point, I think you should be able to cancel it any time you like and without any diplomatic penalties to third parties.
This reacting to warning signs does not have to be perfect. Just compare the situation to the Real World. Some countries can indeed be very paranoid and tend to see conspiracies everywhere. This would not be bad in a civ game, because I think false positives in this case would just add to the diplomacy, e.g. you are moving large amounts of troops against a third civ when suddenly the other ROP civ panics and orders you to get the hell out.
Well, let's pour some advice to the poor AI, then. If a human civ used the ROP sending troops via your lands when would YOU get frightened?
- Very large numbers of troops entering my territory, especially compared to my military strength. Again, the other party might be honest, but why take the chance? Heck, which real country would be insane enough to let a 3-1 overwhelming force enter its borders if it does not have to? It would amount to occupation even if not intended...
- Large numbers of troops being at "strike distance" to my cities and my defensive troops. Strike distance being here the movement possible in one turn.
- Foreign troops concentrating in "defenseless" areas, i.e. most of my troops are somewhere else.
And lastly, just to make things more interesting the ROP deal could include some modifiers, like:
- Being able to set the max allowed number of foreign troops at any one time inside my borders.
- Restricting the deal with "no-go" zones, like never going close to a city (e.g. 1 or 2 squares) or never enter the city radiuses of the cities X, Y, and Z.