deleteRow() is a native javascript method, but by calling your function the same name it appears that you are redefining it, sending the code into an endless loop as you call the function from within the function. depending on what value
<%=rs.getRow()%> gives, you may not even need that function, and could just call deleteRow() from the button and be done with it. More likely, though you would want to rename the function and do something like this:
Code:
<input type="button" name="b1" value="Delete" onClick="deleteme(<%= rs.getString("department_id") %>);deleteR(<%=rs.getRow()%>);" /> //also note no need for a submit button here
function deleteR(id){
document.getElementById("tableborder3").deleteRow(id);
}