When I said Doctors Without Borders has never allowed combatants to operate from their hospitals, I meant combatants cannot fight their war from or store weapons in MSF compounds. Doctors Without Borders will treat anyone who needs care including Taliban fighters. This is standard practice for medical NGOs. Even the U.S. and Israeli militaries provide medical care to wounded enemies.
The SCUD missile scenario is a difficult one, but a few thoughts come to mind. It is possible that any strike on the SCUD missile will miss, and then you have the worst all outcomes: hospital destroyed + SCUD missile being launched. SCUDs are very inaccurate and may wind up hitting an open field if launched at a long range target. I realize that is little comfort to a country facing SCUD missiles, though, so an air strike might be justified. But that wasn't the case in Afghanistan, Yemen, and Syria where three MSF hospitals have all been bombed in the last year.
Zool makes a good point about justifying something. As the saying goes, if all men were angels there would be no need for laws. If armies always policed themselves and never committed heinous acts, there would be no need for the Geneva Conventions and other laws of war. Everyone always feels their acts are justified in the moment. ISIS fighters feel they are justified in beheading non-Muslims. The angry husband who catches his wife cheating feels justified in killing her. We cannot rely on an individual's sense of justice in order to prevent terrible acts, especially in war.
You cannot be a law unto yourself, there must an external, neutral arbiter. That arbiter is ex ante the Geneva Conventions and other laws of war. That arbiter ex post facto is the War Crimes Tribunal in the Hague, and to a much lesser extent, each nation's criminal courts. I think everyone on SDF agrees to the necessity of rules of war so our differences lie in how much discretion to grant each military commander and soldier.