Can an air traffic controller refuse to give service to an aircraft based on moral grounds? Today I learned about a Twitter account that tweets arrivals and departures to/from Geneva, of aircraft used by dictators.

I was wondering if an individual air traffic controller could refuse to give service to a given aircraft based on moral grounds, without legal consequences? 

Maybe I'm a pacifist controller and I prefer to not handle a military aircraft sending troops somewhere. Or I don't like dictatorships and I don't want them in the country/airport where I operate.

Is there any legislation that could protect such objectors? To narrow a little the question, let's stick with Geneva in particular, or Europe in general.
No.

The purpose of air traffic control is to prevent collisions and expidite and maintain an orderly flow of air traffic. An air traffic controller has no say in who gets to fly and who doesn't. Refusing a certain flight would be something that needs to be done at a political level, and certainly far away from an operational level.

Also remember that, except in special cases, air traffic controllers have no way of knowing who is onboard a certain aircraft. Essentially, all we see is a flight ID and a route. Air traffic controllers are not in contact with passenger lists at any time.

Furthermore, air traffic controllers do not have any physical way of preventing flights from taking place. See this slightly related answer: Can a pilot take off at his own discretion?