During the USSR this was not any bigger of an issue than say, pollution in China in the 90s and 00s. Not good but not the catastrophe it became after the USSR dissolved.
And China managed to turn its ecological problems around within less than a decade. If the USSR was still around they would probably have already completed a megaproject to bring the entire sea back.
Development always comes with a cost. Sometimes it is necessary to make a short term environmental sacrifice in order to lift millions out of poverty.
If the USSR had not built the vast irrigation network in Central Asia, these countries could not have developed modern agriculture on the scale that exists there now, without which the level of urban and industrial development they have now would have been impossible.