WD40 should be safe to use on rubber but it eventually evaporates so it's effectiveness stops. A silicone spray should work better as it will lubricate for much longer. But clean metal on rubber shouldn't squeak so maybe you should try cleaning (de-greasing) the piston first.
I think its the rubber squeaking when it is compressed as the pedal is pressed down and the piston moves in an out. Its one of those little annoying noises that once you have heard, you tend to concentrate on !
Will give a squirt of Silicone a go and see if it lasts longer!
Used to get this on Corsas sometimes, and on the Seicento a long time ago. Both of these it was the pedal pivot that was squeaking, quite a tedious job removing the pedal pivot and regreasing. Obviously wasn't the pushrod seal on the Sei as that was cable clutch.
WD40 is not a good lubricant as it gets pushed away easily. If it is the pushrod seal, proper brake grease would be the best option, local car accessory shop will supply, usually in small quantities.
If it is the pedal pivot, only real cure is remove the pedal pivot and grease properly. Just looked at Haynes manual, seems straightforward, as long as you can stand on your head in the footwell. Removing the seat makes it easier, but a longer job.
Got some silicone spray and gave it a squirt of that a couple of weeks ago - did the trick - hopefully it will last longer than WD40 and is probably safer for the rubber.
Know what you mean about the standing on the head ! Got myself stuck trying to get in to spray the silicone - being over 6 foot does not help - glad the neighbours were out !
Did you mention you can get a Haynes manual for the 500?