I just killed Rattus to see what he had. (I'm doing the bank thing anyway) I got Rubber Shoes from him. Any use for these things?
Are there any other drawbacks to killing him; should I reload prior to his death?

You can make a search for the shoes. I was told that they have a use in Mine Tunnels, but nothing important.

Killing Rattuns makes the Razuka hostile (Milano and Don)

You're never going to see Rattus Rattus again anyway.