How can we distinguish an honest and good scholar from a bad and misleading. I used to think before that they are all honest so I didn't understand why Islam was telling me to be so evil. It also makes me confused because why would someone dedicate so much time for the sake of Allah to be a scholar and then be misleading?
Scholars are humans and are subject to all the forces and temptations that cause humans to be unjust at times. Sometimes out of anger or a personal dislike for someone, a person may feel strongly tempted to say or do something unjust.
As for finding who the best scholars and thinkers are, even the pagans of Mecca recognized the good and honorable character of Prophet Muhammad 
even though they rejected his mission. The reason they could do that was that they saw that the Prophet never lied, had impeccable manners, never broke promises and never betrayed anyone’s trust. Truthfulness and honorableness are characteristics that are relatively easy to discover in people.
Judge Muslim scholars and intellectuals according to their manners and character and how much they are like the best people mentioned in the Quran. Trustworthy Muslims do not scoop down to personal attacks. They are polite, even toward the rudest of people. They do not get angry. They admit the limits of the evidence instead of trying to convince you that their opinion is correct. If a Muslim is desperate to convince you of something so that you start to feel uncomfortable, as if they are trying to convince you to make a leap of faith and to submit to their opinion, that is a very strong red flag that that person is not trustworthy.
Trustworthy Muslims respect the fact that you are an honored human in the sight of God whose dignity and conscience are inviolable, they consider you a respected human whether you agree or disagree with them, while untrustworthy Muslims consider you an instrument; if you agree with them and submit to them, they will be nice and kind, and if you refuse to do that, they become rude. They are tribalists who only consider you a proper human if you belong to their “tribe” (sect, madhhab, etc.), and if you do not belong to it they treat you as if you were subhuman.
Above I have described the extreme examples of trustworthy and untrustworthy people. Most people fall somewhere between the two extremes since no human is perfect, so how much you trust someone should depend on how close they are to the trustworthy or untrustworthy side.
If you are sincere in your faith and you have the Quran to guide you, it would be easy for you to distinguish between those who are most trustworthy and those who are least. Those who fall victim to misguided and harmful doctrines generally do so because of flaws in their faith; they follow a person who offers them a lax version of Islam that helps them continue sinful lifestyles or one that offers them wealth, connections or glory, and they choose to follow them despite the warnings of their intellect and conscience. In Islam, since you have been blessed with an intellect and conscience, you are considered responsible for who you choose to follow. Saying “I followed the wrong person” is not a valid excuse, because you are considered sufficiently intelligent and capable to distinguish between trustworthy and untrustworthy people yourself (there might of course be rare exceptions). In two passages (2:165-167 and 34:31-33) the Quran mentions God rejecting the excuses of people on the Day of Judgment who say they were only following others.