If you're running a program in Java that connects to itself on a remote system, could you not just do an RMI (Remote Method Invokation, I think) to tell the client version of your program to start itself and do its thing? If you have a version of your program on the client machine as well, I don't think that the antivirus would be a problem. Unless you're explicitly writing a Java program to install something on the target machine, in which case, you probably can't do it, because if you could, then it would be just as easy to install viruses on a remote system.
The goal really is to work in harmony with an antivirus, not to subvert it :)
I'll ask a lot of questions (most of them probably stupid stuff). Bear with me, i'm still learning! ^_^ Also, I'll try to answer as many questions as I can as well, but I'm not very good yet. I'm sure I'll be of more use once I get better :)