Yes, since the mandate is a tax, they could use reconciliation to ditch the mandate without being able to be stopped by a fillibuster. But presumably, it couldn't be used to ditch the ban on discriminating against those with preexisting conditions. The insurance companies will lobby furiously not to ditch the mandate alone. Whereas if the mandate had been struck down by SCOTUS, the GOP wouldn't have to worry about that, because the court would have done their dirty work for them.
Even if the mandate is ditched, health care companies can still raise the premium prices to offset the risk of preexisting conditions. Are the health care companies bound by making their premiums "actually affordable" are they restricted in price increases by the new law?