Organizational Policy = no reference letter from employer

[surefire]

I just found out that the NGO that I'm conducting policy research/analysis for, as an employee, has a broad organizational mandate which forbids supervisors from writing reference/recommendation letters.

I'm kind of baffled and bummed (bammed, if you will). I've got two great academic referees (MA thesis supervisor and a MA theory/methods prof. who has agreed to supervise my PhD research). These two will certainly suffice for current grant apps; however, a few actual program apps need 3 letters. I've been away from graduate studies for a year, doing some awesome research work in my field. I was REALLY hoping to show off some of that experience via a reference letter from a supervisor. I was hoping to leverage the experience to demonstrate some relevant, transferable, "real-world" research capacity and prove that my time away was well-spent... I thought that this would help to distinguish my app.

Now I'm kind of bammed. I had an earlier contract involving similar work with a different NGO (that supervisor would be thrilled to write a letter for me). But that earlier contract was part-time, short-term (4 months), and in a smaller organization; while the current one is full-time, longer-term (will be 10 months when my contract is up) and in a very established, respectable organization. (I think that the "established" thing is part of the letter-writing hesitancy; my sense is that, they don't write letters because they usually employ people for many years and like to protect themself from any negative association with a previous employee who doesn't ultimately stand up under scrutiny. They are a very large organization with a lot of accountability and a highly-valued brand, I guess I appreciate the motive...)

Anyway, I'm wondering if anyone has had a similar experience or is packing any advice. I'm concerned that admission committees might think it's odd that I don't have a letter from the most recent, relevant and prestigious work experience that I will have had on my CV leading up to application deadlines. Is there a way to pre-empt this? Could I notify the program director of the organization's policy or does that just seem pedantic?

Thanks in advance for feedback!