Thinking about the ideas you bring up.. it seems we humans have been playing on the same level as the bacteria upto now. Greedy algorithm vs greedy algorithm. Could we perhaps use certain antibiotics that will force bacteria to evolve in a way that opens up a certain weak spot which we will then allow to spread through their population before we step in and wipe them out using this forced back-door? This simple 1-2 plan seems enough to really cause evolution a problem if humans can coordinate enough to pull it off (and a plausible plan appears, details..).