On one hand, we want someone running the FDA who has experience with the food industry. (Just as we would probably prefer having a manager who has spent time in the trenches coding).
On the other (tin foil hat) hand, has the food industry placed a 'friend' in charge of the people that should be regulating them?
He wasn't put in charge of the FBI though and I'd assume he had heavy oversight.
Treasury, SEC, FDA, FCC, etc. They're all stocked full of cross-overs, that go from private to public and back or vice versa.
I don't think there's anything tin foil about it at all. It's de facto how the system works. I don't think it guarantees how a person will regulate, but it does probably trend toward heavy bias.