It would only have been repugnant if Jonathan requested people not to do what Sam did. But the game had no rules and what is deemed a good or bad outcome is purely subjective. Who's to say free coffee for some is better than charity with this experiment?
Just because the majority dream this specific experiment to be something that it isn't doesn't mean someone who comes along and dashes those dreams is an asshole.
If you want his actions to be deemed repugnant, then setup a new Jonathan's Card experiment, define the rules the way you want with the no-scraping clause. Then wait until Sam breaks those rules. Then you can call his actions repugnant.
EDIT: I'll admit it's probably not the nicest thing to do if he knew that people (wrongly) assumed their donated money would go to buying coffee for others. But the risks were clearly defined and anyone donating money should have realized that their money is actually going to the experiment, and not necessarily to buying coffee for someone.