This question just popped into my head yesterday. I guess it might be too basic (or too impossible) for EL&U; but I thought I'd give it a shot.
How come these two words managed to evolve to different spellings? Surely in the days when the grammar nazis ruled the earth with their gimlet eyes and blood-red pens, they should have caught this?
deign - c.1300, from O.Fr. deignier (Mod.Fr. daigner), from L. dignari "to deem worthy or fit" (cf. It. degnare, Sp. deñar), from dignus "worthy" (see dignity).
disdain (v.) late 14c., from O.Fr. desdeignier "disdain, scorn, refuse, repudiate," from des- "do the opposite of" (see dis-) + deignier "treat as worthy" (see deign).