In the model of planned behaviour, in between the 'intention to performing an act' and 'performing the act', I believe conscience is a significant factor that may or may not aid the performing of the act. (See the Figure below)
You have asked a good question, but I don't think that the answer is going to be easy. FIrst, you have to analyse just what you mean by intention in that context. Variation in intention will have a strong confounding effect on your measurement. Is the intention because of ethical imperatives or financial inducement, and so on? The next thing to consider is the nature of conscience in your model. To use it you must have some sort of metric of conscience and a way of measuring it, and neither of these are going to be easy to do. It isn't clear either, if conscience should be an input to 'intention' or a modifier of the output of 'intention'. You will probably have to make an arbitrary decision here and just stick to it. But I wish you well in your researches!
Where conscience functions in the area of ethical decisions can only be for some in some cases. There are a complete range of ethical decisions and decision making made that do not involve or consider conscience. We are here perhaps in the area of memory, of the recollection that we harmed someone who perhaps we should not have done. That involves therefore awareness of harm being done-again some share this, others don't.
Suppose, for example, you are recruiting a work force for a company and someone comes to you for work-they have a family to feed who are reaching starvation, and are desperate, but are not the best candidate. As a recruiter surely you are ethically bound to employ the best worker. Several of the man or woman's children die, who might have been saved by your actions. You can put that down to fate. Ethically, you did the right thing according to your work role. Others might feel differently. Would conscience have crept in if you had employed the man/woman, their efficiency was low and the other workers were affected, and the project suffered? Would you have had a conscience over not helping the man or woman-that surely depends on your perceptions of life, the way you were brought up or ethical viewpoints you embraced later in life.