First, it doesnt happen all the time. It wasn't like that when one of my daughters visited last week and when I visited in November. If it becomes a regular issue, there are ways that Disney can deal with it.
Second, if I have to wait outside for 2 minutes to get past the scanner, I am OK with it. If I need a poncho for those 2 minutes, I'm going to need one anyway.
Third, who has established as a fact that FP+ is slower. The reports on that have been mixed at best and our family's firsthand experience has been that there is no difference. If you mean that it takes a few seconds longer per person to get past the scanner, who cares if it doesn't affect how long it takes to get on the ride.