According to the way the ACA is written they can ONLY take a penalty from your tax return. So the simple solution is to pay exactly the amount you need to in taxes and not have a return. Or defer taxes until tax season (if your responsible).
Careful here. The penalty is CALCULATED on your tax return. The bottom line is what you either owe or get refunded. If you owe the penalty, you owe it. And don't think they won't get it from you just because there is no refund to deduct if from.
Also, I have seen people say, "I'll just pay the $95". The penalty is $95 OR 1% of your income (not sure if gross, AGI, MAGI, etc), whichever is more. Next year it is $350 or 2.5% of your income.