I've done it without realizing it. PO left the drain open on the intercooler tank for some reason. I think it's the reason my intercooler pump died about a month after buying the car. So while its possible, I wouldn't recommend it.
Yes pull the fuse on the intercooler pump you don't want to run it cycling nothing. I don't recommend driving it that way but if it is not a long distance and it's a must some times you got to do what you got to do.