A paintball gun would solve the paint getting into the props or backwashing all over your drone but I'm certain the FAA would frown on such a thing.
Don't even think of Dropping something or Especially using a paintball device ( big Heck no from The F.A.A. ) Many of the A.M.A. ( Remote Control Aircraft ) Flying fields around here have tried to get permission from the F.A.A. to fire paintballs at each other via remote control or have dogfights and shoot at each Other. Every time the F.A.A. has told them Basically "Don't even try it". One of these flying fields is way out in Mojave nobody around for 20 miles and they still said No Way.
And the biggest thing that kills the Idea is that you will be spraying a chemical from an Aircraft requiring God knows how many permits from the E.P.A.-F.A.A. -F.B.I. you see where this is going.....
You'd think with all the chemicals Agricultural drones spray on crops, that a few paintballs would be ok'd by the FAA. But I can see why they wouldn't want to open that potential can of worms...lol.
A paintball gun would be a great idea for practicality, lower cost (muuucch smaller drone + other benefits), but yeah I looked it up for here in Australia, probably the same in the US ???
Are paintball pistols legal in Australia?
Paintball Shooters Licence.
Paintball Guns or Paintball Markers are a firearm in Australia. To buy a Paintball Gun or Paintball Marker you must have a PTA (permit to acquire) or your relevant state equivalent. Remember to obtain a shooters licence you must have completed and passed a firearms safety course.
But, it still might be possible to make a paintball marking system, let me explain . . .
They make paintball
pistols.
Strip down the stuff that makes it look like a gun, set up in retro type fab frame, like a 'naked' paintball pistol.
Thinking how they do this for GoPros on FPV drones, strip away to outer unneeded casings, the call them 'naked GoPros'.
Or, there might be some sort of Co2 apparatus one could make a 'one shot' device that takes a paintball.
Obviously a pistol type capacity setup could fire who knows how many paintballs on a flight, so maybe a better way to go for the OP if marking numerous spots on a flight.