The FAA would be reluctant to be seen as "meddling" in what's considered a civil employment case. However, the FAA responded by moving up a comprehensive audit of Allegiant's operations (CHEP audit) after this incident and others.
Allegiant's next CHEP audit wasn't due until 2018. Instead, FAA gave Allegiant an audit notice in March and FAA auditors were at Allegiant for three months from April through June of this year.
Allegiant passed the audit with only minor issues flagged and no enforcement actions required. Some of the issues were really minor like one training room apparently had its AC temperature set too low that it was found to be distracting. Allegiant had until this past Friday to address the issues and apparently they did so.
I can't speak for Allegiant pilots, but note that after a tough period they have just won their first union contract (CBA) including up to 30% pay raise and promised improvements to safety processes + culture.
Allegiant is also replacing their aging MD-80s and moving to an all-Airbus fleet by 2019. They recently placed an order for 12 brand new A320neos -- the first time in history they've purchased new aircraft.
So I think Allegiant pilots (now among the best paid in the industry) have room for optimism. They used safety as a "stick" during the contract process and now that concessions have been made it would not be in their benefit to criticize.
If I recall it was noted previously in this thread that Capt. Kinzer's suit was filed without involvement from Allegiant's union (Teamsters).