Applying to work at a non-profit where I was recently a consultant

I recently applied to work at a large, multi-national, conservation non-profit. I previously worked as a consultant for said non-profit for a year and a half. While working as a consultant, about 30% of my time was spent working for them. I was a low level employee and not privy to the bid process or any kind of contract negotiations. I left that position over a year ago and have been working in a completely unrelated position since. Now, a great opportunity to work directly for the organization has come up in my desired location. I fit all of the desired qualifications of the job and know the position very well since I had previously being implementing the on the ground work. In my application I listed my previous supervisor at the consulting firm as a reference. I also checked a box that noted a "potential conflict of interest" that I would have to disclose or clear up in the interview process (checking the box doesn't remove an applicant from consideration).

Now I'm second-guessing using that supervisor as a reference in case the non-profit sees that as inappropriate. The application window is still open and I'm considering changing my references to reflect my concern. Do you think a hiring committee would see my previous experience with the non-profit as a positive or as a conflict of interest?

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