Warranty is a great thing if you have it, but as said if they think your the one at fault by running the tank well past the low fuel alarm, then you may be stuck up the creek and up for a new pump.
BUT, most models have a low fuel alarm, at least my VS does, and if it was meant that you were to fill up at 1/4 tank they would tell you somewhere in the users manual to do so, ignorance can be an excuse if you were not told at any time.
I would push for the warranty repair especially if the low fuel alarm never went off, mine did it once but I was only 50 yards from a servo, my pump sounds like a very quiet electric motor and is only heard faintly with the radio off and windows up when first turning on the ignition where it fills and pressurises the fuel rail.
The light on the dash lights up when the low fuel alarn goes off, and goes out when you have fuel in the tank showing you the system is ready to start.
Leave your handbrake on lightly for 100 yards, it's the same alarm and you definitely won't miss it, the thing scared the crap outa me.