Corrupt behavior of government employees is already illegal, so if your concern is that they'd approve R&D funding for a drug and development company they have a financial stake in, that wouldn't be allowed and would be dealt with, unless they can prove that the drug really should be developed and the company getting the contract and funding really is the best choice.
Same goes for the manufacturing side, once the drug is approved.
And for the approval process, what perverse incentives would be created that don't already exist, and are already being dealt with? Today, anyone at the FDA who approves a drug that they've got some way to benefit from is already breaking the law.
>what perverse incentives would be created that don't already exist
If the FDA is both in the business of facilitating R&D, and regulatory QA for the products resulting from said R&D, you're creating an internal feedback loop that results in a couple predictable courses of action for the organization to appear successful:
1. The R&D program 'picks winners' and puts low-hanging fruit in the product pipeline that's highly certain to pass QA. FDA looks good due to high % of approvals for products it pushes to develop, but doesn't really reward innovation or high-risk + high-payoff projects. While this yields benefits, it doesn't address the issue of trying to get 'moonshot' type projects that result in significant leaps ahead funded.
2.) The R&D program (predictably) suffers from the same sort of high failure rate and safety issues that plague pharma in general; it's not a fault of the FDA per se, but because our collective knowledge regarding mechanisms of action is still rather basic. FDA proceeds to be attacked by Congress, the public, the media, etc. for 'wasting taxpayer dollars' on a low-yield program. FDA officials are thus incentivized to let their standards of quality and efficacy slide in order to protect the agency's image on the R&D side of the house.
The organization will "appear successful" if it brings useful drugs to market at a reasonable cost to patients. There would obviously need to be unbiased criteria for deciding what's useful and what isn't, and the decisions around both selecting criteria and applying them should be made by medical professionals, not bureaucrats or MBAs.
Your second argument could be applied to every government program, which are attacked all the time, with the intent to get rid of them and eventually have no government programs at all. That's a separate problem that needs to be solved.
