Remember when Xykon killed a bunch of self-righteous Paladins...

[Jason]

Personally I take that just as a requisite to qualify for the template in the first place, not as a subsequent restriction (the way druids, paladins or bards have alignment restrictions). The Libris Mortis might say that a non-Evil lich is a conceptual oxymoron, but it still says they can exist, which is all that matters here, since nobody is saying they're common or likely, just that they're possible.

The way it's written is not really "these guys totally exist in your standard D&D world," it's more like "If you the DM really really want a good lich, despite the fact that it shouldn't be possible here's a way you could do it."

Edit: Libris Mortis also contains another reason why creating undead is an evil act. All undead are powered by the negative energy plane, but they are also a sort of minor gateway to that plane that siphons off energy from the prime. So every undead you create permanently drains a small quantity of energy from the world and hastens the effects of entropy in it. Creating lots of undead, or allowing lots of undead to continue to exist measurably shortens the life span of the prime material plane.