I think you don't understand.
Checkpoints are not there to fight proof of work - they are there to protect your node from DoS attacks.
Do you understand that if there were no checkpoints, anyone with a graphic card could just keep mining blocks that link to the genesis one, and this way fill up your hard disk?
Do you understand that checkpoints completely violate the entire purpose of Bitcoin?
What they do is introduce a form of approval(consensus) about the state of a chain. This form of authority could certainly be abused, and it runs counter to practically every design principle of Bitcoin.
at the most fundamental level, the client code should not have ANYTHING to say about the block chain. Whether this is required in order to operate is irrelevant. The reason people use Bitcoin is *because* it's peer-to-peer.
You are free to use and distribute a fork of the client without any checkpoints. Checkpoints aren't required. Assumming an attacker isn't attempting to DDOS your node by filling it with years worth of bogus blocks or try to perform a 51% attack months deep in the chain the lack of checkpoint will have absolutely no effect on your node.
So if you are worried then remove the checkpoints, compile it and use that node. If you are really worried set up an online mirror and advertise your checkpoint free version.
See peer to peer at work.