I think you may be stuck. Systems with single-button mice are supposed to be able to use alt-click to simulate mouse button2. Essentially, an alt-click
is a button2 click and vice versa. (Same deal with meta-click and mouse button3.)
I don't think there is any way in the AWT/Swing APIs to distinguish between an alt-click and a button2 click.
All that InputEvent.isAltDown() does is
test the ALT_MASK modifiers bit, so will behave the same as testing that bit yourself. (InputEvent is the parent class of MouseEvent.)