I’m surprised that “swan song” isn’t listed in your dictionary. Mine, the Merriam-Webster’s 11th Collegiate Dictionary, defines it literally as “a song of great sweetness said to be sung by a dying swan” and figuratively as “a farewell appearance or final act or pronouncement.” At any rate, I don’t think that “swan song” was used by Ms. Pedrosa in its semantically correct sense in that sentence. She might have meant “mistaken idea” or “rationalization,” as in this rewrite of that sentence: “President Aquino’s unconscionable use of power is encouraged by the mistaken idea that this is the way forward for the country.”
Also, I think it’s incorrect to infer that by using “swan song,” Ms. Pedrosa wanted to convey the idea that the unconscionable use of power is “that one big thing or achievement that Aquino will be remembered for even if he’s no longer president.” My feeling is that she really meant to say that it’s neither the correct way to make the country go forward nor a desirable thing for a national leader to want to be remembered about. By the mistaken use of “swan song,” however, this sense was lost in the rendition.
As to the phrase “not that I know of,” it definitely doesn’t mean a categorical “no” and it doesn’t mean “I guess” either. What it means is “not that I’m aware of,” as in this conversational exchange: “Did the senator really plagiarize those passages from the blogger’s website?” “Not that I know of, for I haven’t read the senator’s speech and the blog yet.” Of course, the sense would be downright wrong if the reply was “No, for I haven’t read the senator’s speech and the blog yet.”
As to your last question, it’s not right to say that the past perfect tense can never be used alone in a sentence and it’s not right either to say that the past perfect tense should be used sparingly.
It’s true that the typical past perfect sentence consists of two separate actions in time, as in this sentence: “The ship had sunk when the rescue team arrived.” The earlier action takes the past perfect (“had sunk”) and the later action takes the simple past (“arrived”). However, the past perfect can also be used alone to denote an action that began and ended at some indefinite time in the past, as in this sentence: “The heavy floods had lasted two weeks.”
Clearly, there’s no point in prescribing that the past perfect be used sparingly. It will always be called for when the action had taken place and was completed at an indefinite time in the past. When the precise time is given, however, the simple past tense must be used: “We met at the park yesterday.”