I think it's a very sensible change that wouldn immediately improve the game. Is it realistic? No, ...
On the whole, I think the Original Poster makes a very good point -- two points really -- regarding AI Player movement on roads within human-controlled territory, and Human Player movement on roads within AI controlled territory.
For my part (perhaps because I am a more casual player, who is not looking for a game with suicidal-masochistic ( i.e. "challenging", "hard", or "ridiculous" ) levels of play, I am more concerned about the former. In other words, I WANT the AI Players to not be able to use MY roads as super-highways, to crush me at lightning fast speed.
However, the principle quibble I am raising in this reply, is that it IS REALISTIC to reduce or remove road bonuses, for roads that are not controlled by the side/player that is invading territory that is not their own. Historically this has always been true. Moving through enemy controlled territory means (some examples): the roads could be guarded by partisans; the roads could be partially mined (which doesn't effect the owner of the roads, because they know where the mines are); the roads may not be well known (well mapped); the roads could be otherwise compromised (semi-scorched earth policy, on the part of a retreating enemy); and (most basic of all) movement is slowed, because the invader will tend to be cautious simply because they are dealing with an unknown. This is basic psychology ...
Of course, E:FE is a fantasy game. But given the UNIVERSAL nature of slowed movement (reduced speed of movement) in enemy controlled territory, it is "realistic" to incorporate the same feature in E:FE. Once outposts are destroyed, and cities are captured, the territory reverts to friendly (or at least, nuetral), and the road bonuses could be restored. But until then, road bonuses in enemy territory should not exist ...
(AND I take Steven Aus's last point regarding harder levels of play: if you really need to allow AI players to use road bonuses, without limitations, on the "challenging/hard/ridiculous" levels, you can leave that in. But on lower levels, road bonuses in enemy territory (especially for the AI players, IMO) should not exist.) That would be more realistic ...