It makes sense to treat fortification as an action that uses up the unit's movement for the turn. It's not like fortifying a military unit is just a matter of them crouching behind a bush, after all. The presumption is they are using up their turn action by actually building fortifications on their position, such as digging trenches and so forth. I don't see the problem in requiring the player to use up that movement just as he would for a unit actually moving in order to get the defensive bonus of the fortifications--you can't change your mind when you move a unit and take it back, either.
The reason it would not make sense to allow moves to be "undone" is because moving a unit has an effect that is not reversible. By moving a unit, you might reveal information about the surroundings (e.g. spot an enemy) that you can't just get rid of by undoing the unit's move.
With fortification, it would only make sense to use up the units movement points if there was something irreversible about the fortification action. As in my example, if the fortification of a unit gave a combat bonus to an adjacent unit, that would be an effect that cannot be reversed so undoing the fortification after the combat bonus has been taken advantage of would be an exploit of the feature.
Realism argument here is completely irrelevant. I know it takes time to build fortifications in real life.
Unless there is a good reason to do so (which I'm trying to figure out), forcing units to run out of movement points when they select fortify is about as arbitrary and annoying as forcing you to move units in the exact order they were built, or to not being able to select a unit with the mouse but only be able to cycle through units using the < and > keys.
So, do you see my point about the difference between actions that are reversible and those that are irreversible?
Examples of reversible actions in civ4 were: Sleep, Fortify, Sentry, Sea Patrol, Air Intercept Mission
All of those actions had something in common - they did not have an immediate effect on the current turn - the action could be reversed.
Examples of irreversible actions in civ4: Movement, Attacking, Build a tile improvement, Bombard, Pillage.
All of these had an immediate effect during the player's turn, one that could not be reversed.
Blockade in civ4 was an interesting one. Theoretically it could be reversed because it didn't have an immediate effect during the player's turn, but its implementation was such that the unit's turn would end with that action. As I said before, there may have been underlying reasons to do this, like avoiding computationally demanding trade-route recalculations.