OK, after researching the topic a bit, I think I can make someone here very, very rich with a patent (share some of that money with me and don't be a scrooge, ok??).
So what we need is a high resolution camera that can detect the presence of a medium to large sized bird in front of the engine in a matter of milliseconds. Upon detection, a massive airbag is deployed that is too big to enter the engine. At the same time the engine will automatically shut off. When there is no suction left due to the completely shut down engine, the airbag will naturally fall down, at which point the pilot can restart the engine. The airbag on its way down, upon reaching a certain drop velocity can then deflate through the automatic activation of a self puncture mechanism.
Yes, this all sounds very expensive. But it could be cheaper than losing an engine and replacing it, or the entire aircraft, not to mention loss of life.