I'm unconvinced that SC is actively doing something to throw clans under the bus.
The March 2016 MM update may have been the biggest long term mistake they've made, even bigger than the sudden change to the shield system in December 2015. Getting back to more realistic weights is helping, but the problems heavily engineered clans present to finding a really fair opponent. Those clans will cause problems for the MM until SC decides they won't match a clan that is too unique to find a fair opponent for. I'll have to remain skeptical of any claims of match fixing on SC's side, until clans like the Martians are unable to maintain long win streaks.
SC at least seems to be aware of the issue & may be deliberately moving slowly rather than making yet another sweeping change with unforeseen consequences. It also seems that they are finally realizing that the war scene is the main draw for most long term players, not trophy pushing.
I've been nudging them on social media to figure out something besides war & trophy pushing to retain the end game players. The community is been doing a lot to pick up the slack by creating our own tourneys & the CWL. SC needs to hire a couple people to help run the CWL & probably a few more to run special events to keep people engaged with the game.