The article makes a point of comparing the mergers to the broader economic conditions at the time. HP acquired Autonomy and lost money at a time when the computer industry was (and still is) growing.
On the other hand, AOL and Time Warner merged right before the bubble burst and BoA acquired Merrill Lynch at the same time the economy was crashing. Without the acquisition, Merrill would have gone bankrupt anyway and BoA's market cap would have cratered anyway because the entire financial sector was cratering at the same time. In fact, the US government heavily pressured (threatened) BoA into acquiring Merrill (http://www.washingtonpost.com/wp-dyn/content/article/2009/04...).
Of course they are "different cases" - there are always separate macroeconomic conditions, and there was government intervention in the acquisition, but the fact still remains on the "worst corporate deal ever" front, BAC acquired a company that lost $20+ billion in the first post-acquisition quarter.
They are not comparable. Its good info and context, but you're overselling it as a comp. "worst corporate deal ever" is shorthand for executive decision. ML was too policy infected to be considered a "real deal" with other options on the table. If you take the "choice" away from the transaction, you are no longer takling about a "deal" in the common sense of the term, IMHO.
On the other hand, AOL and Time Warner merged right before the bubble burst and BoA acquired Merrill Lynch at the same time the economy was crashing. Without the acquisition, Merrill would have gone bankrupt anyway and BoA's market cap would have cratered anyway because the entire financial sector was cratering at the same time. In fact, the US government heavily pressured (threatened) BoA into acquiring Merrill (http://www.washingtonpost.com/wp-dyn/content/article/2009/04...).
So no, they're much different cases.