Infiltrating the other player's city with your meeple is potentially useless with just two players. Most of the times I've seen it happen, neither player gained the advantage and the city was completed with both players receiving equal points; might as well not score at all then. If that doesn't happen, the city sometimes goes completely unfinished with almost all meeples ending up inside it.
If you are in the lead you should almost always try to score as much points as the other from his/hers cities. If you are not in the lead you should obviously try to not give away points.