... Real airliners have fielded automated systems to avoid birds? Nope...
I am a big airplane nerd, have a license and many type ratings for interesting aircraft. I also do a lot of systems engineering. There are not many systems that intervene and take action on behalf of a human. You can find various kinds of fairly-static control loops on aircraft (autopilots, pressurization systems). There's some things that take immediate protective action, like circuit breakers. You can find things like stick-pushers that will apply forward pressure to the stick/yoke after some time of warning of an incipient stall.. You can also find things like envelope protection / more advanced "do what i mean" control laws on Airbus.
But when there's a fire on an airliner, it's almost always the flight crew that pushes the button to discharge the fire bottle. When there's an incipient collision, it's a flight crew who listens to the order from TCAS and decides whether to comply.
The thing is, yes, computers are really good at responding to understood, common failure modes. Aviation accidents have progressed beyond understood, common failure modes to esoteric strange events. This is because we've augmented human ability with CRM, automation of routine things, additional alarms and alarm prioritization, etc, etc, etc. Remaining failure modes exercise the redundancy in unanticipated ways-- like someone taping over (and not removing the tape from) all 27 static ports on the aircraft and the static ports leaking air out but not allowing air in. People are good at problem solving and figuring out what is going on in those types of circumstances. Machines are very bad, currently, at that type of anomaly detection and resolution.
There are times that having a human in the loop means a human does something stupid and kills everyone aboard. E.g. AF447 (though I wonder how well a machine would do, because the Airbus fell out of the more sophisticated control laws to a base level of automation because of the contradictory sensor readings). There are also more times when a human with a high level of systems knowledge and troubleshooting.
Overall, the philosophy is this-- We make the flight crew behave like a machine under ordinary circumstances, with a lot of automation of routine flight and decision support and checklists. When things go wrong and off the scripted checklists, we instruct the flight crew to use the automation if possible (autopilot, etc) and to troubleshoot systematically, to communicate with each other and divide up manual responsibilities, and to effectively question each others decisions while keeping on the problem.
This is what the human factors crowd and the NTSB have decided is the best path for aviation for the foreseeable future. Perhaps you know better? Even Airbus, who is on the leading edge of having the computers do more and more, doesn't go anywhere near as far as you describe.