Leaving a pool covered for a season and through another winter
There should be no permanent cosmetic damage unless you have something seriously wrong with your liner (in which case the damage is already done).

Replacing water is very rarely the solution for algae.  In practice you can just leave it until next season.  Of course make sure it's winterized &mdash; i.e., if you're in a freeze zone ensure all lines, pumps, and filters are clear of water; and pump the water level back down.

If it were me I'd probably also dump in a "winterizing" dose of KemTek 60% algaecide, and if you have any metal in your water or pool also a winterizing dose of stain preventer.

But there's nothing you can do to have clear water when you open it in the spring: It will have to be started up, vacuumed, balanced, etc.