Hrm, if you think about it a bit, most of the time you probably want to reorder ships instead of doing a swap. Since crew gets added in a priority scale down, most of the time your fleet will be sorted already.
So when you'd want to change the order would be when a new ship comes into the picture and it needs to fit somewhere along the line.
It seems to make sense that the default behavior would be to insert (as the op said) rather than swap. Maybe another option is to just add some up/down buttons that slide it up along the list... or maybe at the end of the day the ships should be displayed in a 'fat list' with the ship picture on the left and ship info on the right of a line, and you move ships up and down in the order with some buttons or drag and drop.