I don't think one's conscience is necessarily reliable. Each person is different and sometimes feelings of wrongdoing can be programmed right out of your conscience.
Take for instance simple things. Let's say when you first started driving, you were maybe conscious of the speed limit and maybe felt concerned or guilty when you went a mile or two over. Then, you discovered nothing happened when you were driving 5mph over. So now your conscience is saying "that's OK". Nowadays when the speed limit is 55, but you're driving 70 to keep up with traffic and don't feel bad about it, what happened to your conscience? Is it still there telling you this is wrong?
Same goes for any other thing that you've come to accept because "everybody else is doing it".
And you've got to incorporate your upbringing into your conscience. What makes one person feel guilt may be perfectly OK elsewhere. Does that mean one is wrong or living a bad life? In Germany, many public beaches are nude and people walk around with no guilt or shame. Yet here in the US, people's consciences tell them it's wrong or it's a sin to be nude in the company of the opposite sex (except spouses). Or, switching it around, in Afghanistan, some women's conscience may make them feel guilty if they don't wear a burka. Yet here in the US, how many women's consciences tell them that?
I think so much of what our conscience tells us is learned behavior. I don't believe that our conscience is some universal meter of right and wrong that transcends learned laws and practices. It's learned from laws and from religions and other forms of influence. And, when people talk of a Biblically trained conscience, that's exactly what it is - accepting the Bible's rules (or more likely a specific religion's rules) as the triggers for feelings of right and wrong and guilt.