I was thinking the same thing. The border penalty is so ridiculous right now I'd prefer to just turn it off and go by the honour system. Is that something that's even possible or is it built into the core code?
If you have a neighbouring city the AI warns you about a couple of units in your own territory. They don't even give scouting units a break, put a scout near an AI border and you get a -1 diplomatic penalty... even if you have open borders! And the range which they detect you seems to be about 2-3 hexes. One game I had open borders with Hojo and was healing three scouts by his territory, got the big diplomatic penalty for not moving my troops when I promised so I loaded an auto-save from 2-3 turns ago. I moved the scouts and pretty sure I had them at least 3 hexes away, but it still triggered.
This is becoming my biggest pet peeve, as you're basically getting negative diplomatic points for simple early game exploration.