I don't know if it would ruin the membrane, how long did you run it the wrong way round? Thinking about it, the membrane is only a super fine filter so I shouldn't think it would destroy it. What could have happened is that raw water going through the wrong way may have left a deposit of dissolved solids on the 'wrong' side of the membrane, so initially water passing the right way through is picking up this deposit as it emerges from the membrane.
I would run it for a couple of hours, flushing for five minutes every 30 minutes and see if it improves.
What's your input TDS?