I have to approach this question from a purely philosophical sense. But I think the phrasing and the questions Nemo poses are really for the philosopher to answer. Not the pastor or the rabbi. Not the theist or atheist.
1. If it's a flawed way of thinking, what harm is it causing? A puppy doesn't die each time a person has a flaw in their thinking process.
What is a 'way of thinking'? Is it a process of belief formation? It is a world-view?
To be a proper epistemic agent, we hold ourselves to a standard. We don't generally accept tarot card readings as justified beliefs simply because they don't reliably get us to true beliefs.
And that's essentially what we want - justified true beliefs, i.e., knowledge. We want to avoid flaws in our reasoning and thinking because we want to be good cognizers. If someone uses flawed reasoning, wouldn't we hesitate to believe anything they say?
Now, I'm not saying the theist is flawed in all her reasoning. But to ignore a potential source of false beliefs is not doing your duty as an epistemic agent. Flawed thinking is intrinsically harmful to our web of beliefs and allows for skepticism to take a very firm hold of our situation.
2. Let's say that religion does effect a choice they make. You can either a) tell them God doesn't exist and have them put up more resistance or b) feed onto their beliefs in God and change their mind on whatever problem they are causing.
What kind of a choice are we talking about? There are certain choices that can be motivated by religion, like volunteering at a soup kitchen, that we typically wouldn't fault someone for making. But the point you're trying to make here, while correct, misses the real issue. If we can somehow physically prove that God doesn't exist, then religion can no longer be a justification for any particular decision or belief. At this point, whatever the theist is trying to do doesn't get off the ground because it isn't justified. An analogy here would be that I decide to go pick clovers because I want to feed the unicorns. We know there are no unicorns, so the justification for my actions just doesn't make sense. I am deemed at this point to be irrational.
The crux of this is that, even without God, there are other reasons to do nice things. Of course, there are also other reasons to do bad things, like try to purge an entire group of people. The issue still comes down to what actions are justified, and without God we lose a type of potential justification.
If a theist is against homosexuality, who cares?!
A lot of people do. Now, if it's just their opinion and they don't act on it in any way, then that's one thing. But this simply isn't the case for nearly all people.
Most people against homosexuality isn't doing squat to keep gay marriage illegal.
They are voting. They are protesting. And if they're not protesting, they are lending support (at least in the form of justification) to those that are. If there were just 20 or 30 people protesting something for some asinine reason, we wouldn't acknowledge their claims on any real level. But the religious right has done much to politicize and they are very good at achieving their agenda. It's a grassroots campaign that is meant to appeal to a specific population of Christians.
It's easier to persuade an anti-gay christian that God supports homosexuality than to persuade one that he doesn't exist.
Again, this is ignoring the question at hand. The question is why we should seek to disprove God's existence? Or at the very least we can show the theist's beliefs to be unjustified - the result is epistemically the same.
We're not trying to rationally convince the theist of anything. If we can establish one of the two claims I just mentioned, then either the theist abandons his belief in God or risks being considered irrational.
A similar analogy is the now-extinct belief in spontaneous generation. There was evidence for it and many people believed it, but it turned out to be false. Any decisions or justifications based on this erroneous claim would be irrational (at least after the claim was shown to be false).
Yes, people use Religion to justify their choices. Sometimes they justify good, sometimes they justify bad.
Again, if we show that a concept of God is false or irrational, then any justification thereof would also be irrational. Again, your claim, while correct, is missing the point.
To sum up, we want to know whether or not our beliefs are true. This is one of, if not the, primary goals of responsible cognitive agents. The points you are making describe the world as it is given that we have no proof either way of God's existence. But with proof - either positive or negative - comes another solid cog in our ever-growing web of beliefs.
In either outcome, given the truth (or falsity) of God's existence, other statements will logically or inductively follow. We open an entire world of new beliefs with the verification of just this one belief.
But let's keep in mind the project: to disprove God's existence (according to the OP).
To a philosopher, to prove or disprove something is to do so deductively. Unfortunately, there are two types of statements that cannot logically be proven: negative existential statements (eg., God doesn't exist), and positive universal claims (eg., all ravens are black).
The real project is to show the notion of a western God, as it is currently conceived, is somehow self-contradictory, unjustifiable, irrational, or some combination of these. While the project may never be completed by philosophers, it may be something that society eventually just accepts.
