Negotiations during the due diligence period can be a tricky ordeal. If there were competing offers you could risk losing the property if you ask for changes depending on how the contract was written. Assuming it's just you and the seller and no other pressure or competing bids then you have an advantage since you have something the seller wants (money) and he can't get it unless you give the okay to move forward.
In Real Estate, if a seller is aware of an issue with his home, he needs to disclose that to future potential buyers. If you discovered something he wasn't aware of and inform him of it, it becomes part of the disclosure process going forward now. So, even if he won't fix it for you, other buyers are going to have the same issue with it so he knows he'll have to either address it with you or someone else. He doesn't have a choice.
Basically you need to decide what is fair and form a plan. Inform him of the issue and decide what needs to happen in order for you to proceed to closing. Give him a path to the finish line. (i.e. 50/50 on the repair or drop the price or whatever). You can exchange ideas with your agent and have him work something out with the other side through conversations but once you all agree on a plan you MUST GET IT IN WRITING so everyone is legally bound and your EMD and interest are protected. An addendum to the agreement is a common tactic for this that everyone signs
If I was the agent here, I'd advise my client to just ask for the repair to be completed to 100% satisfaction and see what they come back with. If they agree, then done. If not, then they'd need to come up with a plan we'd be happy with like: Have us get 2 estimates and get a credit at close equal to the lowest one or something. If they 100% refuse to deal and its take it/leave it, then you need to decide if you're willing to buy the house with that issue. If not, then you walk and find a more reasonable seller.