How much time have you got before you depart? if you've a week or so and can access your european passport authority in person, they can annotate the "remarks" section of your wife's passport to record that her married name is "x". the customs/immigration people ought to be fine.. as the other posters record, your problem really only lies with the airline. i'm called by my 2nd christian name not my first, and the office has on occasion booked in under the 2nd initial/name causing the airline to claim i'm a different person. bring all your documents and allow plenty time to escalate to a manager/supervisor. consider how you will escalate if they still don't budge (photo of culprits for the suing them under the small claims court for unreasonableness; quote legal statute at them, and so forth). but be calm and measured!!!
good luck!