If the timechain fees scale upwards to incentivize chain security as the block reward gets lower, then privacy solutions like coinjoining needs to scale in upward layers.
I wouldn't be as worried. It's definitely a shift, yes, and a time of transition where it's tougher to gain on-chain privacy, because there's little focus on on-chain privacy AND coinjoins aren't as active.
Split those up. 
Stronger focus on privacy on the chain is paramount, but we can achieve what coinjoins achieve through upper layer protocols.