Realizing that Saul had become hopelessly corrupt, Samuel separated himself from Saul. But Samuel didn't go around fighting Saul. He didn't go around "warning people about Saul's sins," or "exposing the sins of King Saul." Samuel mourned for Saul; he didn't hate Saul, he loved him. Incidentally, I have personally observed that the people who leave a church because of sin in the leadership often love the pastor more than the "yes men" who tell him what he wants to hear.
It could be argued that Samuel should have stayed with Saul. Samuel could have been a good influence on him. That's the course that Jonathan took, and God did bless Jonathan. But Jonathan also got destroyed along with Saul.
After a while, God gave Samuel a newer and greater ministry: to make David king. Your Christian life will not collapse if you leave a church for the right reasons. If innocent people are hurt by your leaving, that is the leaders' fault, not yours. Your Christian success ultimately depends on God, not men. The fact that someone is angry at you for doing what is right does not obligate God to stop blessing you. God blessed Samuel after he left a bad leader, and God can do the same thing for you.