I have no problem with it. I have no particularly loyalty to an alignment system, but I have always insisted that some sort of 'alignment system' is good for an RPG. I'm rather fond of the Nature/Deamenor system of WoD, for instance, and I'm particularly fond of the fact that you are rewarded for acting out your nature. The force point/darkside point system of the WEG SW system was another naturally game enhancing alignment system.
One of the problems I have with GURPS is that it is rather lax about its strictures. That can be fine, but I've found it takes a better class of player to RP well in a structureless system like GURPS. The best thing it has going for it is 'quirks' but unfortunately they have no real mechanic, and thier main purpose is to remind the player that he does indeed have a duty to role play.
The most obvious problem I think you would run into with an alligence system is that the system would become watered down by a large number of possibile alligences, especially if those alligences become quite vague.
For myself, as an opinionated fellow who takes things rather seriously, I have a whole lot of allegiances.
I have allegiances to my wife, my family in general, my God, my country, my personal honor, and a whole realm of personal beliefs from economic principles, to philosophical positions, to favorite TV shows I'd passionately defend. Some of those allegiances are more important than others. I won't die to keep B5 from being disperged, but I'd certainly die to protect my wife. Do we need allegiance heirarchies? Do we need to assign weights to allegiances?
It might make some people more comfortable to call things 'allegiances' and get away from the notion of absolute good and evil, but in the end I don't think this additional level of percision is going to simply things all that much. It might make people more aware that there are different flavors to say 'good' or 'chaotic' or 'lawful', and it might lead some people to understanding of greater complexity than D&D's system, but in the end I think you'd still end up with people having debates over whether or not someone was being true to his allegiance.
Take the often debated example of a Paladin. Does it really make it any simplier to say that a Paladin must have an allegiance to a code of honor (law), and a set of benevolant moral virtues (good)? Aren't we still going to debate what that means and where the lines between just and unjust, honorable and dishonorable lie?
One of these days I'm going to have to sit down and write up an alignment system that is as complex as most systems combat systems, just to show it can be done, that it can be interesting, and why you'd probably want to avoid 'realism' in alignment systems unless you wanted to bring RP to a screeching halt while you rolled dice to adjudicate it.