For the color blind, simply changing the colors.color file (See Carbon's post for the location) with the appropriate colors you want fixes it for you. It's absurdly simple to fix that and it doesn't affect your checksum so online play is unaffected if yours is different then someone else. If you visit here: http://www.december.com/html/spec/colorhex.html or any of the other literally thousands of places on the net that give you hex color codes, you can find new colors that work and since the file in the core game is in text format, you have to do absolutely no converting of files. Know what color needs to be changed (0 through 9), find a color that works for you, change the value FFabcxyz (always preface it with FF), save, play to confirm you're good with the change, done. Most mods do not touch this file, but those that do, the process is exactly the same only change the file in the mod folder. And before you ask or attempt it, no you cannot have more then 10 colors.
As for the icons, a post was made in DS informing people that we'd make and include custom icons in the mod for anyone who wanted one. Only the lore people answered, and not even all of them. So there are custom icons included in the game, and from personal experience, it's not really a requested feature at all, especially if a mod as popular as DS offers to do every bit of the work except for making the final decision on which one you want, and no one really answered.
The problem with an automated process is how Sins handles things. First you need an image in gray scale. This controls the shading of the faction color on the icon. Then you need an alpha layer cut out that matches the icon so that color can be applied to it as well as tell the game what parts of the icon to display. Multi color icons are handled by adding color to the gray scale image itself, but if I recall correctly, your faction color will mix with this color changing it to a third color so you really have to work at this to get it to show up properly and anyone not using the color you use for it gets a messed up color instead. Back to that alpha layer cut out, it needs to be copied three times over in three additional sizes so it can be displayed properly in the many places your faction icon shows up. Once you have all of that done, you need to change the 5 player theme files many sections to account for all of the new icons, and then when that's all done you have to distribute it. It can either be done by constantly adding icons to a file, assigning each one a unique ID so that the next time you play and someone is using that icon, it reappears and an active player ends up with a massive file, or pass it around at the game load for every single game and these changes are all made on the fly. Either way, there are too many ways an automated process can screw this whole thing up considering everything that needs to be done and load times would most definitely increase. While some games simply take an image and overlay it on top of their skins, Sins uses a far too complex method to make this happen easily. So I doubt this feature will ever show up no matter how much supposed interest there is for it.