Which is they Geneva Conventions and other treaties of the like make it clear that the protections only apply to groups that have signed and follow them.

The proto-ISIS militia groups in Iraq did not, and would deliberately target civilians, refused to wear uniforms, and hid among civilian population. Because of that they did not have POW rights that afforded to legitimate militias.

Refusing POW rights is as much a reflection on those they fight as it is on ISIS. If you're making categories like this you have crossed the moral line, if not the legal one.

POW rights are earned by wearing uniforms. Not wearing uniforms means you've passed a moral line that encourages the murder, if not slaughter, of civilians.

That may be legally correct but is that morally ok? How do you apply this to groups history looks upon sympathetically? French partisans come to mind, but there are dozens of other groups that had similar situations. Selectively deciding abuse of humans is ok is a slippery slope. Not wearing a uniform may relate more to total oppression or occupation rather than be an indicator of disregard for civilians.

Yes, it is absolutely morally OK, because it puts pressure on all combatants to follow conventions designed to protect civilians.