If a unit that has the pursuit ability chooses to use it, does the additional attack have to be against the unit being pursued or can it be against another unit? I ask because the reference book states that the pursuit attack is considered an "additional attack" and according to the reference book additional attacks can target units not targeted by the normal attack.

Going by the rules it seems like a pursuit attack can target another unit but the concept of pursuit makes it seem like it should only target the unit being pursued. Any thoughts are welcome as this issue popped up in a recent game and I conceded that my citadel guards, when pursuing can only target the unit which they pursued and I don't think that is right.

Indeed, you can attack any unit you want. The only restriction while resolving pursue is that the first hex you move must be the hex the unit you routed / destroyed occupied when your first attack was resolved

Well, there is one more restriction to resolving "Pursue" if you have Pursue 2 (IE, the Flesh Ripper Brutes): You can't use the second move to go back into the square you originally occupied. You don't have to use the second space at all, though, you can just move the one space and attack from there if you want.