My sympathy - You find yourself in an awkward position with your employer. Ethically,when they accepted the money, they agreed to implement their proposal.
It's understandable when, on occasion, an agency fails at implementing their plan. (Isn't failure often how we learn?) But accepting a grant calls for responsible communication with the funder about progress and problems, and a mutual decision about how to proceed - or cease - activity.
As a free-lance grant-writer, I'm often in a position to 'fill in the blanks' as I'm writing a proposal. When I email my draft, I ask the client to read it for accuracy and content. I remind them that they will have to live with what I've written, so they better be comfortable with it - or tell me how to adjust it.
I have, on two occasions, decided not to take additional assignments from clients. In one case, like your's, the client didn't behave responsibly once the grant was awarded. In the other, after developing a grant for a consortium, I felt the lead agency wasn't competent to execute the grant,
As a free-lancer, I have that freedom (and I treasure it). I have other clients. As an employee, you're in a somewhat different situation. But, I encourage you to take your talent elsewhere.
Good luck finding other work. I find that if a good percentage of your grants are successful, and your clients find you easy to work with, the work comes to you.