I quote from Tarantino "From Dusk til Dawn" (god knows why I do) to explain why Mephisto would want Kurt out of play in the final fight.
"As far as God's concerned, we might as well all be a piece of shit... but he is one of the boys."
Of the core X-men group, Mephisto would have 3 major opponents, if the big battle final to pass. Jean Grey (host of the Phoenix), Ororo Munroe (descendant of a former Sorceress Supreme with latent but natural mystic abilities) and the most dangerous of all to him - Kurt Wagner. Not just a mere loyal believer, but a full on "man of the cloth". Kurt's faith would be a rallying point for the "Forces of Good", and with the might of heaven unleashed against the fury of the burning abyss, Kurt would be a natural focal point for such energies, making him a seasoned front line soldier in which the spiritual fight would be just as important as the actual physical combat.