There are two alternatives:
1) You can drain the pool down so that there's a foot of water left, put on high rubber boots, and scrub the exposed walls. Be sure to make sure you support the walls from the outside, like with tent ropes and stakes.

2) You can use Poconos' method of water exchange, involving covering the entire surface with plastic, and putting new water in on top as you drain the old water from the bottom. This keeps the liner stretched and prevents the walls from imploding.

Or you can spend a little bit of money on bleach to clear the water and not risk having to replace the liner.