The accounting department loves you. I’m sure the government will bow down to your demands, respect your security concerns, and adopt a more secure approach swiftly.
If you must deal with an organization that doesn’t give a shit about security, then you’re SOL. We live in the real world. If you don’t submit the government forms how they want you to, they shrug and fine the shit out of you. They couldn’t care less about the security risks their workflow poses on you.
You can mitigate the risks, but you never have absolute control. While Acrobat poses a security risk, not having Acrobat poses a business risk.