I was always of the opinion the SEC was going to focus on the ICO scams. Not the legimate projects that may have not done things correctly at launch. However, the second they went back in time and forced the legitimate players to pay back the money accepted (in fiat dollars), it changes everything. Tons of ICO projects likely have to dump bitcoin and ether to satisfy this.
I honestly would be surprised if action is taken against tether or bitfinex. A conflict of interest fine maybe, but if there was something as big as you and others think, the CFTC would have found it when they launched their investigation almost a year ago at this point.