(a) For heaven's sake, talk to her about this. By far the best possible option is a two-layover route, especially if you'd be scheduled to arrive more than three hours earlier than the existing EWR-XXX nonstop. If you get lucky, you might misconnect and hit the EC.261 jackpot.
(b) If that's really nonnegotiable, take BER-EWR-XXX anyway. Four hours at the airport isn't nearly as bad as you're making it out to be.