Two pieces of advice. First, approach the evaluation in terms of program improvement, as opposed to judging the value of what the organization is doing. Talk about the evaluation in those terms. Second, remember that the people that make up the organization are the real experts on what they are doing -- if there are problems they probably already know about them. If you approach the evaluation collaboratively, they will be more likely to accept the findings and be willing to work with you to identify and implement solutions. Your job is not to fix the organization/program but to help them collect systematic information and help them to use it effectively.