If you need to keep historical data for the addresses these keys represent then you cannot delete them (by deleting or moving your wallet.dat file to another location) as bitcoin doesn't support yet a watch-only wallet functionality that would allow you to check on addresses that you don't currently own (there is a pending pull request for watch-only wallet functionality:
https://github.com/bitcoin/bitcoin/pull/4045 so I hope this really cool feature will be added soon to bitcoin).
On top of that, bitcoin will not use these addresses since they are empty (so they don't hold any unspent outputs) and since it generates a new address for every outgoing payment you make, so the only case these addresses will ever be reused automatically is if you ever receive any funds to them.
In the case you don't really need these historical data on-line you can stop bitcoind, delete your wallet.dat file (or move it to another location), then restart bitcoin and a new wallet.dat will be generated, fresh as new, which will offer you a peace of mind.