Re: I have a bad reputation
Money is a great lubricant for diplomacy in RTW. If you can spare the cash you can often secure a ceasefire with 10k or so of hard cash. May seem like a lot of dough to hand out to a tiny nation to stop them fighting you... but if you can get trade rights going again you can often make the money back anyway.
Generally I find it's better to let the enemy enter your provinces everynow and then. It's usually obvious when they're going to siege a city as opposed to wander aimlessly through your lands. Before I've driven away a potential attacker simply by doing the same to them, parking an army next to one of their cities. They often withdraw their army when you do that. The other alternative is to bribe away trepassing armies.
Re: I have a bad reputation
I say kill 'em all!! :charge: I now have neither patience nor mercy for armies passing through my lands. The whole PR and diplomacy is, as we know, not quite as flawless as we'd want it to be. Just as most of the micromanagement part of the game. So, I just cannot be bothered and will slaughter any intruders.