Not taking sides, but there are some facts to consider:
The pump is designed to stay submerged inside its own bucket regardless of the fuel level in the tank. I don't know what it's called, but through that whole mess on the assembly, suction created by the pump sucks the fuel from the tank through the bottom of an outside bucket then it's dumped into the inside bucket that the pump is inside of. This inside bucket stays filled and the pump pulls from that to feed the engine. Also, they pull from the bottom, so it's already "sucking all the crap at the bottom", anyway. these pump run for hours and hours on end while people sit idling, creeping in traffic, on road trips, etc. They're rated at something like 150 or 190 LPH (I don't recall exactly), which is 40-50 gallon per hour. Based on these numbers, if you were pumping down a full tank, you'd have it done in about half an hour. But, I'm sure that doesn't account for the restriction of the fuel lines, etc. So, lets just double it. I'm sure the pump has an hour's run time left in it.
You could set it up and find something else to do, just keep an eye on it to shut it down as soon as it starts sputtering. It'd be nothing different than if you were running the engine for an hour or however long it takes. Might wanna keep a battery charger on the battery, though.