They can't get rid of RWT unless they removed free trade again. Operation ClutterFlusterer is just targeting the bots you see ingame, particularly the gold farmers.
This will most likely have a significant impact on the RWT market if Jagex actually succeeds. The price of gold will likely rise because there will not be nearly as much of it being pumped into the game anymore. This is all assuming that the bot-nuke is successful though.
Jagex has a reputation of shitting the bed when it comes to things like this, and most of the well known scripters have a reputation for being extremely good at what they do. So we will just have to wait and see what happens.