There are two things you can do to try to preserve your independence, and as you mentioned, your reputation.
One is by using internationally recognized methodologies. In the contractual arrangement and discussion we had it was very clear I would follow this methodology and I expected to be able to go to the country and have free access, etc. The second element is around the transparency of the report. That allows the public at large or interested stakeholders to make their own assessment of the assessment. In the absence of an independent body that will fund these, I think that's about the best you can do.