Jews weren't popular in Renaissance Europe. (We know, you're shocked to hear that: The Jew of Malta is so full of praise.) They frequently faced the decision of either converting to Christianity or being expelled from their country. Remind you of anybody?Ferneze's Convert Or Fork Over Your Wealth bargain, even though it sounds crazy, would have sounded relatively normal at the time The Jew of Malta was being performed. But the ordeal didn't end with conversion. There was a lot of paranoia over whether or not these Jews had really converted or were still practicing Judaism in secret—being obdurate. Barabas is a prime example of exactly what the Christian world was losing sleep over. He absolutely refuses to convert, wholeheartedly embraces every horrendous Jewish stereotype, and is really, really (really really really) hard to take down.
Barabas has to die, because once he moves from wanting money to wanting control of Malta, there's nowhere to go but down.
Despite his professed maniacal will to survive, Barabas loses, instead of gains. The play suggests that maybe compromise is the way to go.