Generally, a buyer can assume that he is purchasing everything connected to the house except for items explicitly reserved by the seller.Therefore, since the halachah prevents the seller from removing his mezuzot, the buyer can assume that they are included in the price, unless the seller indicates otherwise. Moreover, since nowadays the price paid for a house is extremely high, the buyer can legitimately claim that he didn’t expect anything unspecified to be removed.
It looks like your buyer had done a little research and saw that since the mezuzot were obviously more expensive than standard ones, some authorities would support your position that the buyer should assume that they were not included. So as not to benefit from a doubtful situation, he felt that he should at least pay you the difference between the price of the expensive mezuzot and the price of standard mezuzot.
If you feel uncomfortable accepting the check, perhaps you can discuss a compromise with the buyer or, better yet, the two of you can jointly donate the money to support Torah study!
 Shulchan Aruch Ch. M. 214:11.
 Pitchei Teshuvah Y.D. 291:8, citing Shivas Tzion 110; Mezuzot Beitecha 291:10; Agur B’ohalecha 42:29; R. Eliashiv, He’aros Bava Metzia 102b.
 Teshuvos V’Hanhagos 3:465.
 Shevet HaLevi 2:159; Teshuvos V’Hanhagos (3:465) examines this dynamic.
 Kiddushin 59a. See Meiri, op. cit.