Another consideration - though a very difficult one to quantify - would be opportunity cost. For the players that "made it to the big leagues", but produced negative WAR, you introduce an "opportunity cost". In other words, we have someone a chance to play in the big leagues that didn't make it. That is an opportunity where we might've been able to find another free agent (yes, budget constraints) that could've produced better (even league average 0 WAR is better than negative) for those seasons.
So not only did we incur the negative WAR, we missed the opportunity of trying someone else there too. A double negative on those players and a painful impact of the 2011 draft.