Shakespere I believe in Hamlet wrote "thus conscience doth make cowards of us all" as far as I know empirical evidence stops around there. Though Dan Ariely in Predictable Irrationality claims to provide evidence that thinking about integrity reduces our tendency to behave dishonesty. His stated experiments are unpublished (in peer reviewed journals), and not conducted to be statistically robust.
In reality, it is obvious that some people behave with greater self restraint and greater insight into group net benefit than others. It follows that conscience is, at the very least, describing an aspect of social behaviour that moderates selfish actions where net negative effects on others are considered. It is easy to see the benefits of such a behavioural trait in evolutionary terms.
The issue then is really at what point does this become a destructive or non beneficially restrictive trait - you can always have too much of a good thing.
Does conscience exist? - yes.
Do we have robust evidence for its benefits? - probably.
Do we undestand its role in social interaction? - not to any useful extent
Have we any method(s) of determining when it is functional versus dysfunctional? - no.