Almost -
Did you get the impression that this was the intent of the "don't discourage" comment, or are we inferring bad intent where none exists?
Well, my honest opinion is that it depends on the elder making the statement. Some would say it with the inferrence that it's preferred that they don't go to the authorities until it's handled by the congregation first. Some would even share scriptures about slander and/or the two witness rule. That would cause some to think that they may be doing something wrong spiritually if they inform authorities based on an accusation.
However, I also knew many an elder (including me) who would say exactly what I wrote above in #3. I would then further explain that this meant they have every right to go to authorities and the elders, the congregation... anyone who happened to know about what was going on would not think any less of them. No matter what their decision, we would be supportive of them and continue to deeply care for them. In other words, we stand by them whatever they choose to do. The only caviat I would mention is that I couldn't make a recommendation as an elder either way as to whether to tell authorities or not. But, again, whatever their decision, we would support them.
I could tell that sometimes my lengthy 'rant' about how they could go to the authorities would make other elders nervous and uncomfortable, but they didn't typically say anything in front of the person.
I hope this helps. Feel free to ask more if you have more questions.