If someone else has a "oh have a look in bank?" type remark then go that but I will go how I would approach things should I want to do something like. I don't know this game but later ones I liked.
So it sounds like alignment is a variable you can control and will be stored in saves, memory..... Just like health, experience, gold...
Time to make a cheat then. Standard cheat making practice -- do a search, change the variable, do a search, change the variable until you find where it is.
Once you have the variable you can then simply make a cheat to hold the alignment value(s) at either max or some sane level. It could vary between leaders or it could be the same and the individual leader value is loaded in when you swap them out (if that is a thing). In either case they will tend not to be terribly far apart or if they are then chances are then it will be in the same relative space (you will have a memory section that holds stats for each leader and it will be ?? bytes into that). By similar token if there is a leader health, exp... stats field then it will be in that so if there is a cheat for infinite leader health then go have a look around that location as part of the cheat making exercise.
As you asked about disabling it entirely then we go further. You still want your cheat however you find the thing that reads this value for whatever needs doing (you do this with a debugging emulator by setting a breakpoint on read aka bpr in most things). Said read will lead to the parts of the game that care about the value. You then have to figure out how to negate this. It could be hard to do, the classic thought experiment we teach to new hackers is Mario losing lives -- you can make a lives cheat easily enough, however you might then have to find what does poison mushrooms, time, enemies, pits, hazards as they will likely all be things that subtract from the lives counter if you are going to approach it that way. I don't know what alignment does but it sounds like one of those luck type variables that subtly permeates everything in a game ( http://elderscrolls.wikia.com/wiki/Luck_%28Morrowind%29
), probably should have looked up a faq rather than looking up luck in a random game but hey cheesy films are calling.
Short version. Make a cheat as it will probably be easier in the long run.