If words are left off at the end of a sentence, and that is all that is omitted, indicate the omission with ellipsis marks (preceded and followed by a space) and then indicate the end of the sentence with a period … . http://grammar.ccc.commnet.edu/grammar/marks/ellipsis.htm
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...
Also, I have no CMS subscription, but here's a public-facing FAQ that seems relevant:
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).
But I guarantee that the journalist deliberately omitted the word "not" to completely reverse the meaning of the sentence.