First of all, if a user does not have access to a document through Section Access, then he shouldn't even see that document in the AccessPoint. There was a confirmed bug in v11 SR1 related to this (bug ID 47615) that I don't think was fixed in SR2. If you contact Qliktech they may be able to give you a patch, I'm not sure.
If you still want to go the route of changing the error text, try to open C:\Program Files\QlikView\Server\QlikViewClients\QlikViewAjax\htc\QVAjax.js, search for the offending text, and replacing it with what you want. There are a couple instances of "Failed to open document" so I'm not sure which one is the one that needs to be replaced. I haven't tested this myself, so let me know if that works.