Certified GKH Gardening Expert
It will not harm your tree in any way. Leaving in that water much longer will. You will need to plant this as soon as possible.
I, actually, prefer to top mine at 2 or 3 feet tall to make it easier to control as it branches out. You can cut it that short, but it will be very hard to manage later on.
This article will give you information on the care of these: https://www.gardeningknowhow.com/edible/fruits/avocado/indoor-avocado-plant-care.htm
As will this one: https://www.gardeningknowhow.com/edible/fruits/avocado/avocado-tree-growing.htm