Yes it can, because of the HHS waiver system. You attack it through the fact that HHS can issue waivers.
Also, what has been lost here is that Roberts ruled that ANY regulatory mandate that regulates "inactivity" is Unconstitutional.
That is huge. That is gigantic. That is worth the price of admission. Think about how much of the Federal Government can be challenged simply because Roberts ruled that you can't "regulate inactivity" under the Commerce Clause.
Keep your eye on the long game. The short term will suffer some setbacks, but this is HUGE in terms of impact on Government's ability to issue regulatory demands.
The first time the Government issues a regulation to just go out and do something you aren't already doing, it can now be challenged using this precedent.
Also, The 16th does allow income tax, but not a tax for inactivity, hence congress' dependence on the commerce clause. Now, thanks to Roberts, they can just call it what ever they want and the court will fix it for them.