If your organization has a Union, you should be very careful in how you handle an employee survey. Here is an article that details what is going on right now between the USPS and the Union.
I bring this up because I was speaking to a consultant friend of mine who is dealing with this exact same issue. In his situation, the head of the Union and the head of HR basically got into a power struggle and the employee questionnaire was caught in the middle. The Union wanted to be more involved in the process and HR did not want them involved. Therefore, the Union was going to recommend its employees not participate. This made for a very awkward situation for my friend as he was caught in the middle and was being asked to moderate between the two groups.
So why am I bringing this up? This is just a reminder that if you truly want to measure employee loyalty and the perceptions of all employees, you need to ensure the Union is on board as well. I have seen it happen before where the Union is not involved or does not get any say in the process and it creates a lot of tension. The sad thing is, when this happens, the employees are the ones who left out in the cold. The employees never get a chance to say what is on their mind and have an opportunity for the organization to address their specific issues.