Yes, they did - as a secondary argument. It lead to the following amusing exchange on the first day of oral arguments (pp 31-32 of the transcript):
"JUSTICE ALITO: General Verrilli, today you are arguing that the penalty is not a tax. Tomorrow you are going to be back and you will be arguing that the penalty is a tax.
Has the Court ever held that something that is a tax for purposes of the taxing power under the Constitution is not a tax under the Anti-Injunction Act?
GENERAL VERRILLI: No, Justice Alito,... "
But that is precisely what the court did in this case!
"JUSTICE GINSBURG: But the question that I asked you is, if you're right that this penalty is not covered by section 7421, if you're right about that, why should we deal with the jurisdictional question at all? Because this statute, correct, the way you're reading -read it, doesn't involve a tax that's subject to the Anti-Injunction Act.
GENERAL VERRILLI: Yes, that is exactly our position.