Personally, I think Elal should asterisk certain flights and say that while they are scheduled to land before Shabbat, they won't go out of their way in the event of delays, and PAX should book at their own risk, or fly on an earlier or later flight.
I don't think Elal should go through the charade of sending new planes to Europe which does nothing to actually prevent Chillul shabbos (and ends up creating more Melacha with now 3 flight crews flying), and I don't think in the future they should make a stop before Shabbos to deplane frum people at all.
I think Elal was in the wrong here, only because over the years they gave the impression that they would protect pax on shabbos, and barely met that commitment. They ought to just be upfront and say any flight with a scheduled arrival within X hours of Shabbos won't be protected.