I have created a server monitor program in Java that connects to servers via SSH and constantly refreshes the new server load every 3 mins. The problem is that even though it is a Java app running shell commands to get the load info, the commands still appear in 'history'.

The question is.. is there any way to return this information without having the command saved in the command history? Sorry if this is a ridiculous question, my Unix knowledge is limited.

You'll need to use a different shell if you want to do that. You can either create a new user to do the job or switch the shell on the user you currently use. sh doesn't keep history and is guaranteed to be available.