When quoting it is permissible to use ... to indicate that you omitted part of the sentence. Standard grammar guides also say that when you end your sentence on a quote, the punctuation mark should move inside of the quotes. Even if it wasn't originally the end of the sentence.
That is exactly what the journalist in question did. The omitted section of sentence was the word not, and it appeared at the end of a sentence.
The Chicago Manual of Style says that "other punctuation [besides the ellipsis, that is] may be used on either side of the three ellipsis dots if it helps the sense or better shows what has been omitted." Then, later, it says "When the last part of a quoted sentence is omitted and what remains is still grammatically complete, four dots — a period [or exclamation/question mark] followed by three ellipsis dots — are used to indicate the omission." And finally, "Three dots — no period — are used at the end of a quoted sentence that is deliberately and grammatically incomplete."http://grammar.ccc.commnet.edu/grammar/grammarlogs2/grammarl...
Wikipedia implies strongly that The Chicago Manual of Style, as well as the MLA and the Bluebook, have different syntactic rules for using ellipsis within a sentence versus at the end of the sentence. That makes no sense if Retric is correct in his/her claim about ellipsis only being licit at the end of a sentence.
These sources appear to confirm my uneducated belief, which agrees with btilly, that ellipses may be used to mark any omission, of any size, including within a sentence or spanning sentences (wp's comment on CMOS implies omitting entire paragraphs is legal).