The unreliabilty of our conscience is discussed in Self-Examination (Study 3.5.5). In any case, our conscience is not going to jump out of us and stand and judge us at the day of judgment. There is one thing that will judge us, the word of the Lord (Jn. 12:48), not how far we have lived according to our conscience. We need to define 'conscience'. It seems to be used by many as effectively meaning 'our inner feelings'. Whether people live according to their inner convictions is not the standard of acceptability with God. We are warned time and again that the human heart is so deceptive that we do not know how evil it is (Jer. 17:9); it is the human heart (not a supernatural 'devil') which leads us into sin and temptation (Mk. 7:15, 21-23; James 1:13-15). Paul says that although he does not feel he has done anything wrong, this does not of itself mean that he is justified in God's sight (1 Cor. 4:4). We cannot, therefore, place too much importance on living according to our natural sense of right and wrong. This is the very error which has led gay 'Christians' to interpret the Bible in the light of their own wayward desires, rather than allowing themselves to be taught by God's word. " It's OK in my conscience" is their only justification. They and many others give more credibility to what they perceive to be guidance coming from within them, than to God's word of Truth. The words of the Lord Jesus in Lk. 11:35 seem especially relevant: " Take heed that the light which is in you is not darkness" . " It's OK in my conscience" is indeed dark light.
And yet there is Bible teaching concerning the need to live in accordance with our 'conscience', and the joy which is possible for the believer who has a clear conscience (e.g. Acts 24:16; Rom. 14:18-22; 2 Cor. 1:12; 1 Jn. 3:21). This must mean, in the context, the conscience which God's word has developed in us- it cannot refer to 'conscience' in the sense of our natural, inbuilt sense of right and wrong; because according to the Bible, this is hopelessly flawed. The fact the " conscience" is " cleansed" by Christ's sacrifice (Heb. 9:14; 10:22) proves that the Biblical 'conscience' is not the natural sense of right and wrong within our nature; for our nature can never be 'purged' or 'cleansed', the believer will always have those promptings within him to do wrong. The cleansed, purged conscience refers to the new man that is created within the believer at baptism. This new 'conscience' is not just a sense of guilt which is invoked on account of not living an obedient life; it is also a conscience which positively compels us to do something, not just threatens us with a pang of guilt if we commit a sin. " It's OK in my conscience" is only acceptable when understood like this.
Thus when Christians claim to be 'conscientious objectors' to military service, we are not only saying that our conscience will prick us unacceptably if we bear arms; we are making a positive statement that our conscience, the new man that has been developed in us by God's word, compels us to positively live a life of love and non-resistance to evil, which compulsion in itself excludes us from taking life.