Just a couple thoughts tonight...this was originally in response to someone's post, but I never finished it and don't quite remember to whom it was originally addressed. I finally finished it tonight though, and just wanted to post it. I hope it makes sense...
1) RE: Catholic Church
While I agree with your notion of not getting too bogged down with the details of the doctrine, I will write a brief opinion of mine about the Roman Catholic Church. As a practicing Roman Catholic, I view the Vatican as a teacher. It may not have the best practices certainly. Indeed, from reading your post (as well as knowing my own perceptions of its teachings), I see once again how perhaps its emphasis on dogma does not always work. Understand though that it does work for others, especially in places where chaos has reigned. Its tough to understand perhaps since the Catholic Church's role is stereotyped in many things, but I think its ultimately a human institution with its own shortcomings and whose teaching style will not work for everyone. Nevertheless, its doctrine is especially important to ward off the extremists/cults who would justify murder or racism because they see the Bible (or say Koran) as saying that they should do it. The Church hierarchy may have made grave mistakes certainly and some of its "rules" are harsh and seemingly illogical. Still, it has done so much good.
For instance, look at the situation in the Philippines. In that country, the church is very powerful and has, in fact, served to uproot (through peaceful means) a dictator (in the mid 80's and to a certain degree, also recently I believe). Perhaps more importantly and more generally, it has also given such hope and meaning to the life of its members. In many instances it inspires altruism by example. Take away the pomp and circumstance of the ceremony and you will see people who genuinely care. If you met the Pope or any of the cardinals on the street without their collar and without them being able to talk to you, you would see by their actions that their heart (more often than not) is pure. Their love of Christ (as with other Christians) has cultivated a certain altruism.
ANYWAY, that's just a brief defense (I'm exhausted and I think I babbled on too much there).
2) RE: free will/prayer/evil
You had brought up some nice philosophical questions there, and a lot of what you say is hotly debated in religious/philosophical sectors (mostly theists though rather than specific Christians).
ANYWAY, this is really what I wanted to write on...the notion of God's passivity. I do believe in free will, like you, and true, I don't believe that prayer is or should be some sort of "genie." I do believe, however, in His intercession. I do not think that God is purely passive. Yes, he lets certain things happen, but I do not think that He ignores our prayers. Looking at my life, I know that I am talking with Him and He is picking up the broken pieces of my life. I have prayed, and to a certain extent, I think all my prayers have been answered. Has my life been easy? No. Was I abused? Yes, of course. Still, I find that the more I truly examine my life, it's not all that bad and in fact, it could have been a whole lot worse. In fact, I feel His presence here, and I know that He has held me up throughout the hard times. It has been a humbling experience to struggle with the abuse, but through my enduring of it, I have learned much about myself, life, and realized that what is truly important is to never give up. Christ felt his cross and knew his death, but instead of not doing what His father asked Him to do, he stuck with it and bore his cross. In the process, he has inspired billions upon billions of people to true altruism. In a sense, he has shown us how to turn an "evil" into a "good."
Having realized this fact, I feel that my prayers have been answered...He has taught me that perhaps there is a purpose to this suffering, and to have patience in bearing "my cross." Does it mean that I have now become some sadomasochist who loves this sadness? Not at all. Pain is pain, and it's not desirable. Still, I know that there is hope. Time and time again, the most horrible pains in my life have been turned into blessings--much like Christ's death (a pain) has been turned into the ultimate blessing (offering us hope).
Indeed, I think that is the one thing that religion, and only religion can truly offer, hope for eternal happiness.