I have to agree with what the other are saying. As a commercial pilot you operate with safety, punctuality and economy as factors to our decisions. The optimal decision for a flight using "the seemingly safest course of action" would be taking off with a plane full of fuel and no payload and only flying on CAVOK days, but that's no way to make money. Standards have been created to operate as safely as it's deemed possible in the myriad of scenarios we might find everyday. From a safety perspective, I reckon it's as safe to take the short or the long runway, so long as the numbers are okay and there aren't other overriding factors (weather, terrain, runway asphalt condition, etc). Otherwise I think the statement we would be giving is that it would be unsafe to operate out of any single runway airport which is shorter than the longer runway in the question we are discussing.
Having said that, and understanding that realistically you aren't always given the choice of which runway would like to depart from (or it's not operationally/economically sound to do so on every single flight), if I'm given the choice I'd take the longer runway just because I reckon it's giving me a bit more wiggle room, in a nutshell.