They would continue to be dealt with through law enforcement like they are now. Drones are a military weapon and would only be used when military action was called for, legal and justified like any other military action on American soil would require.
And yes, drones could target domestic terrorist with minimal collateral damage - less then say a full on military invasion or an aerial assault, but again, this is only an extreme circumstance - one of which we have not had at any point and probably never will. I asked this before and didn't get much of a response, are there any circumstances where the US could use lethal military action on US soil in a legal and justified cause?