As it turns out, Blizzard agreed with this assessment, and the price of Mogu Runes of Fate has now been reduced to 1000 Timeless Coins per Rune. As Timeless Coins seem to be pretty plentiful on the Isle itself, this should make it easier for those seeking to get Runes for further ToT raiding. Killing the rare spawn Evermaw results in over 1k Timeless Coins for the kill, so getting the coins won't be that much of an unreasonable stretch.
In addition to this change, an adjustment has been made for players looking to gain rep with Shaohao -- the daily quest Path of the Mistwalker should now be awarding 250 Shaohao reputation upon completion. While both nabbing Mogu Runes of Fate and Shaohao reputation are still a bit of a grind, these changes ought to make the grind a little more bearable. Whether or not we'll see any further adjustments remains to be seen, but for now, it's nice to know that Blizzard is monitoring the situation and making changes as they deem necessary.