When a city outbreaks when using the Malaria Historical Disease, does it create one or two outbreak cubes?
Infecting and placing disease cubes are different things. It just so happens that infecting often (but not always, as in the case of an outbreak) causes a disease cube to be added.

The rules for Malaria state that you only place an extra cube when infecting. They do not say something like "whenever you would place a cube, place an extra cube".

Rules governing infecting a city:


  To infect a city, place 1 disease cube matching its color onto  the
  city. If there is a purification token in a region adjacent  to the
  city, however, remove 1 purification token from an  adjacent region
  (returning it to the supply) instead of placing a  cube. (If there is
  more than one adjacent region with a purification  token, the current
  player decides which token to remove.) If the city already has 3 cubes
  of this color, do not place a  4th cube. Instead, an outbreak of this
  disease occurs in the  city (see Outbreaks below). Discard this card
  to the Infection  Discard Pile.


Rules governing an outbreak:


  When a disease outbreak occurs, move the outbreaks  marker forward 1
  space on the Outbreaks Track. Then,  place 1 cube of the disease color
  on every city connected  to the city (or remove a purification token
  if any). If any of  them already has 3 cubes of the disease color, do
  not place  a 4th cube in those cities. Instead, in each of them, a
  chain  reaction outbreak occurs after the current outbreak is done


An infected city is only one for which an infection card is drawn.

Regarding your arguments for the other interpretation:

Use of the word "whenever":
This word is used to declare that it happens whenever an infection card is drawn for an uninfected city. I cant think of any other way to describe it without using "whenever" or a similar word. It does not imply there are other situations.

"Infect" vs "infect":
Doesn't matter. Infect is not a proper noun and was not made into one by the rules.

Flavor text:
Given my interpretation, infections ARE more severe.