Per WSJ reporting, they already had negotiated some sort of settlement, presumably with milder action toward all concerned, and then the Tesla side blew up the deal at the last minute, resulting in the SEC's hurried drafting and filing of the complaint we have now.
As a procedural matter, they probably could still settle the case if both sides agreed to do that. But the best deal Tesla could get now is almost certainly worse than what was on offer Monday -- particularly since the case against Musk looks awfully close to open-and-shut.
(The case: 1) He said he had funding secured, 2) he didn't, and 3) the result was to run up the stock price to his personal benefit. 1) and 3) are matters of easily accessible public record; as for 2), Musk thought he could get the money from the Saudi government's "sovereign wealth fund", which was thinking about formally providing it, but had absolutely not agreed to do so. During the BFR announcement, Elon talked pretty frankly about his habit of promising best-case outcomes to give people something to shoort for -- but when it comes to public statements about company financials, it's a very, very, very bad idea.)