Wow, yeah, sounds like they forgot to refill it :/ If it actually _stopped_ rather than some alarm system stopping it then it's probably rooted, good chance that it has spun a bearing or temporarily seized. Have you cranked it over since; does the engine still go round? Would be one thing if it was a car engine where if it dies you just pull over to the side of the road; not so much with a boat engine.
If it had some oil in it I would have said to get an oil test done to check for bearing material in the oil, otherwise someone needs to strip the motor and inspect the big ends, little ends, mains, and probably the cam journals as well. And it very much shouldn't be you that pays for this, as above the mechanic should have liability insurance if they've made a whoopsie.
A friend of ours had something similar happen, mechanic cracked the oil filter housing and the motor ran out of oil on the next outing, mechanic swore black and blue that the engine was fine so our friend said ok if you think it's perfectly good then you shouldn't have a problem swapping it for another motor.
EDIT: If you heard it go "clunk" then it's almost certainly stuffed. Engines don't really have any capacity to go clunk because of the tolerances between parts. When they go "clunk" or "nogga nogga nogga nogga" it's usually because a bearing has spun and shed enough material to open up the clearances enough for, usually, the big end of the con rod to go clonk clonk on the crankshaft. Most of the (car) engines I've seen do this have gone to the scrappy; partly because it's so hard to remove the "glitter" of bearing material that goes all through the motor when this happens.