Why, because they chose to use a kryptonite stiletto?
If Singer's Superman is supposed to jibe so well with Donner's, you could EASILY write the green crystal back into continuity without the audience getting puzzled by the fact that it's green. For example, the green crystal has a freakish glow and a weird humming sound, whereas kryptonite just sits there glowing - heck, in Singer's version kryptonite doesn't even do THAT. Glowing-and-humming green crystal vs. sitting-there-doing-nothing green crystal - shouldn't be too confusing to explain; obviously one's kryptonite and one isn't. And to be honest the more inert version of kryptonite Singer is using actually works to the favor of the distinction - ex: Kal-El not even realizing his powers had been sapped till Lex clocked him.