If the Devil is the Great Deceiver, how would I know that he's not deceiving me through Christianity? I've always been a devout Christian, but I once had a terrifying thought while reading the Bible, and I'm scared I'm going to go to Hell. 

At one point I began to question why God killed so many people throughout the course of the old testament, how he killed peoples' first born children, made people give their kids as sacrifices, flooded the entire Earth and killed almost everybody and everything, sent plagues upon people, burned down their cities and often commanded genocidal wars.

God also commands that everybody fear him and worship him, lest they should burn in Hell for all eternity.

Then, it occurred to me that the Devil is almost never mentioned in the Bible. He certainly isn't credited with killing very many people. He might actually have only killed about ten people in the entire Bible, if I remember correctly. Certainly nothing compared to the millions of people that God kills. 

The things the Devil really did wrong were deny God as his king and try to give Adam and Eve the Knowledge of Good and Evil. I get that, but why is God the one discouraging knowledge? How could Adam and Eve have known it was inherently wrong to disobey God without having first HAD the Knowledge of Good and Evil? Why is it that God didn't want them to have that knowledge?

I remember in Sunday school they referred to the Devil as the Great Deceiver. If he truly IS THE Deceiver, then wouldn't it stand to reason that his deceptive powers would be vast? His capacity for deception would be unparalleled? Could he go so far as to pretend to be God and convince the majority of the world's Christians, and maybe even Muslims, that he IS GOD? Could he convince people to lead crusades and inquisitions? Could he have guided the hand of man to have writ the Bible (and possibly the Qur'an??) for the purpose of striking the fear of Hell into the heart of man and ensuring a future of war and death? To convince everybody that they were wretches without HIM? To make everybody feel ashamed of their thoughts and emotions? Could he have convinced people that knowledge was evil?

I guess what I'm asking, from a vulnerable position is, could God as he is described in the Bible, actually be the Devil in disguise? Why would a loving and all-knowing God be trying to convince people that they should shun and hate gay people or people of other religions? God actually commands people to kill people because they are of different religions or races at different points in the Bible. 

I didn't want to end up hating God as I read the Bible, but by the end of it, I'm afraid I kind of developed a disdain for Him. Even the New Testament, with its morbid demise of Jesus Christ and its prophecies of Revelation, all just seems to be designed to terrify people and make them feel bad about themselves and make them look forward to nothing but a future of fiery apocalypse and uncertainty. It all seems to be designed to make people think they are bad people if they don't follow God's code of law. And then I look around me and I see how hateful most Christians are toward people that are different than them and I assume that the Devil's deception must be working. One day, when the Revelation comes to fruition, and some evil politician wins the Christian vote because he claims to be Christian, I'm afraid it will be the Christians that first follow him right into Hell. I'm afraid I'm already seeing this happening in society today. I'm a Christian that is afraid he has discovered a terrifying underlying message inherent in the Bible, and I hope I'm wrong. Can someone weigh in on this?
By their fruits ye shall know them

Your question is very valid. Satan is the great deceiver, he's been leading people down the wrong path for thousands of years, and he knows that the most elaborate deceptions are 90% truth. Satan discovered long ago that the most effective way to cause people to commit sin, was to make them believe that their actions are done in righteousness, so he sent false prophets to establish false churches that teach the doctrines of men mingled with scripture. He leads them astray with by luring them in with the truth, and then feeding them the doctrines of men. 

Christ warned us about deception: 


  15 ¶Beware of false prophets, which come to you in sheep’s clothing,
  but inwardly they are ravening wolves.  (Matt 7:15;)


Satan has certainly used the name of God to lead many people to do the devils work. Of this there is no doubt, those that blindly followed him were typically deceived by the flattering words of charismatic leaders, many who professed authority from God, who they themselves were most likely also deceived.   

Christ told his disciples how they can know a true prophet:


  16 Ye shall know them by their fruits. Do men gather grapes of thorns,
  or figs of thistles?
  
  17 Even so every good tree bringeth forth good fruit; but a corrupt
  tree bringeth forth evil fruit.
  
  18 A good tree cannot bring forth evil fruit, neither can a corrupt
  tree bring forth good fruit.
  
  19 Every tree that bringeth not forth good fruit is hewn down, and
  cast into the fire.
  
  20 Wherefore by their fruits ye shall know them. (Matt 7:16-20;)


How shall we know them by their fruits? In Galatians chapter 5, Paul explains that a true disciple of Christ is led by the Spirit, and lists the fruits of the spirit.


  22 But the fruit of the Spirit is love, joy, peace, longsuffering,
  gentleness, goodness, faith,
  
  23 Meekness, temperance: against such there is no law. (Gal 5:22;)


Satan CANNOT bring forth good fruit, for "a corrupt tree bringeth forth evil fruit." Therefor you can know with a surety whether a church is led by a true prophet of God through prayer. Only the Spirit can testify of the truthfulness of all things. 


  26 But the Comforter, which is the Holy Ghost, whom the Father will
  send in my name, he shall teach you all things, and bring all things
  to your remembrance, whatsoever I have said unto you. (John
  14:26;)


Trust Only God

You must not trust any man that claims to know the truth without first receiving confirmation from the Spirit that their words are true, you must come to a knowledge of the truth by yourself, through prayer, the Lord will not deceive you. Men will use clever arguments and reason to try to persuade your mind, but you must listen only to your heart for those comforting feelings of love, joy, peace and gentleness. Be careful not to confuse the feelings of the Spirit with pleasure, excitement, pride, or satisfaction, or the like, these are not fruits of the Spirit. Learn to recognize the promptings of the Spirit, and ye shall know the truth of all things.