I must confess, I've only lightly skimmed this thread, but I'm going to go ahead and say that logic is governed by morality, not the other way around.
When I think logic, I think of the economic concept of the rational actor - essentially (it's been a while since I took micro, so my apologies for using Wikipedia to brush up here), a rational actor is an optimizing agent who seeks to maximize utility (stuff that's good for him) and minimize costs (stuff that's bad for him). There are further assumptions about degree of information known to the agent, search costs, and the fixed nature of utility/costs, but for now let's just say that a rational agent seeks to maximize his or her net utility when performing actions.
Now for an example: let's say that there are two candy shops right next to one another. An agent desires to buy a Twix bar. Shop A sells a Twix bar for $1. Shop B sells the exact same good for $2.
Logic (in the form of rational actorhood) dictates that you always buy from Shop A, right? After all, it gives the most utility for the least costs (here easily expressed as money).
Well, let's make this a bit more complex. Let's say that you are a consumer who cares about sustainable business practices, and you know that Shop A dumps toxic waste into rain forests or something - there is some business practice which is detrimental to the environment. Shop B, however, is known for giving back 10% of its proceeds to environmental activism, switching its lights from incandescent to fluorescent, reducing usage of shipping supplies, etc. Now you have two dimensions to logically assess your purchasing decision, and one is less quantified than the other (that is, it isn't quantified).
Let's add another dimension. The owner of Shop A is your best friend, while Shop B is run by a man you are completely indifferent to. You want to support your friend's livelihood, but do you want to compromise your environmental opinions in doing so?
All of these rational appraisals derive from morality, not logic. Logic concludes the vehicle for realizing your morals. Your morals dictate that it is better to support a friend than a foe; logic merely dictates that shopping at Shop A is the best way to do that. Yet a moral system could be devised wherein supporting your foes is more beneficial than supporting your friends (for instance, I want to compete with the toughest opponent possible, since there is no honor in defeating someone drastically weaker than myself, so I will provide my foe with help). You feel morally obligated to defend the environment; buying from Shop B is the most logical way to go about this. Even utility maximization is moral; we care about ourselves as individuals over the wealth re-distribution inherent in higher prices.
Some might say that these morals are logically deduced; that is not true. If they were, then men would reach shared conclusions on nearly everything. Why do students of mathematics ask questions about math and make math mistakes? Because they are learning a system of symbols, expressions, meanings, and values - very roughly speaking, a morality - which is not inherent in everybody. Some may grasp the system more swiftly than others, but it is nonetheless not something "built into" the human intellect, i.e. an objective logic. True, in many of the cases above (for instance, environmentalism), things like human politics can interfere with what appears to be a logical system (environmentalist efforts are countered by people seeking to maximize their own utility in light of this ostensibly "logical" "fact"), but that is simply exposing one's own morality which logic works with to impose order onto the world (people call certain news outlets wrong, but consumers of these news sources probably say the same things about the news sources of their ideological opponents).
But where do moralities come from? Welcome to the social sciences.
This goes further than economic purchases; financial examples merely offer a simple quantified value judgment. Let's suppose that I, as a scientist, discover some new chemical that can be cheaply produced and shipped and grows massive crops. I can solve a hunger epidemic in certain countries.
Then suppose that I abide by Scrooge's saying "decrease the surplus population," where I think that we, as humans, need to trim down our rate of reproduction and the number of us that are on this earth. I might destroy any evidence of this chemical being discovered, and it's totally logical within my moral framework. There is nothing logically which says that I should unveil this chemical; such a presumption presupposes a moral system which values ending human suffering.
If I wanted to be a bit more crass and much more of a fire starter, I guess that I'd say that logic is nothing more than an arbitrary tool for scared men confronting an irrational universe to judge their peers and impose their wills.