As the author of the CIA article, R. C. Jaggers, does not cite any sources, it is difficult to establish with certainty why he used the name 'Operation Salmon'.
The most likely reason may be that Operation Salmon was an earlier designation for Operation Anthropoid (which raises the question as to why he preferred one over the other), but - amidst a fair quantity of literature - there is only one clear reference to this. Therefore, two other possible reasons cannot be entirely discounted, namely that Jaggers used bad or misleading sources, or he did not know the name of the operation and thus invented one.
'Salmon' as an earlier name
It is not unknown for the names of operations to be changed so it is possible that 'Salmon' was the original name for what later became known as 'Anthropoid'.
The only reference I've found for this is an article by the journalist Gian Paolo Pellizzaro on an Italian website Europa Orientale. Unfortunately, there is no clear citation, though some sources are given in the main body of the article. Google translates the relevant section as (my highlighting):
Anthropoid's initial planning was developed by the 2nd Department of
the Czechoslovak Defense Ministry in exile, in collaboration with
Baker Street specialists (named after the Special Operations Executive
headquarters) and the Intelligence Service. The original name assigned
to the operation was Salmon and as a date to carry out the
assassination of Heydrich it was initially thought up to October 28,
1941, the 23rd anniversary of the Czechoslovak independence. But
something went wrong and the plan was postponed ...
Pellizzaro's article does not seem to contain any obvious errors and that 'something went wrong' is corroborated by Michal Burian (2002) in Assassination — Operation Arthropoid, 1941–1942. The drop into Czechoslovakia was originally scheduled between 7 and 10 October 1941 but had to be postponed when one of the men selected for the mission, Karel Svoboda, was injured in training.
Pellizzaro's source for 'Salmon' may be one of two books mentioned in the text shortly before he mentions 'Salmon'. One of these is the Diaries of Sir Robert Bruce Lockhart, but very limited searching is allowed on Google books.
The other possibility is The Unseen War in Europe by John H. Waller. This is also hard to search but, interestingly, the index gives Salmon, Operation, 234 while another page mentions Anthropoid Team, 234-35. Not definite corroboration, but interesting.
If Salmon was indeed an earlier name, why did Jaggers use it instead of Anthropoid? This probably can't be known for sure without asking him, but there are a number of possibilities:
(1) he didn't know Anthropoid was the name finally settled on,
(2) he felt it sounded better in an article which clearly has one eye on 'entertainment' (see below), and / or that Anthropoid might have some of his readers reaching for a dictionary,
(3) 'tradecraft' (as mentioned by NonCreature0714) in his comment, perhaps with particular reference Churchill's instruction on using names "which do not suggest the character of the operation" or
(4) a careless error - there are lots of them in the article (see below) so this may well be the explanation.
Bad or misleading sources
On the second possibility, Marakai's answer has already noted the numerous and obvious errors made by Jaggers. Whether these came from Frantisek Moravec is, though, unclear at best. Moravec's book, Master of Spies, was not published until 1975 while Jaggers' article is dated 1960. The book was in progress when Moravec died, and was completed by his son. Also, some of Jaggers' biggest errors (date of Heydrich's death, the ages of Gabcik and Kubis) are not in the book.
According to the son (in the foreword to the book), Moravec (who was deeply involved in Operation Anthropoid) started making notes on his experiences (in Czech) shortly after he arrived in the US in 1948; he also made recordings and wrote various articles during his time working at the Pentagon. These were used to complete the book.
It is therefore possible that Jaggers somehow had access to Moravec or to something he had written in the 1950s. If Jaggers knew that Moravec was at the Pentagon, it would have been natural to try to consult him given the subject material. Moravec's son might have edited out errors in his father's material before publishing the book, and this could explain why some of the errors in Jaggers' article do not appear in Moravec's book.
Artistic licence or ignorance
The final possibility is that Jaggers, for one reason or another, simply made up the name 'Salmon', just as he made up the dialogues. At this point, it is worth taking a look at where Jaggers' artcle apeared, namely Studies in Intelligence: The IC’s Journal for the Intelligence Professional (vol 4).
This journal contains a number of articles where authors seem intent on displaying literary pretensions by using a writing style clearly not suited for a straightforward report. One article in volume 4 (The Defections of Dr. John) begins with:
Rain streaked the streets of Berlin, splashed on darkened houses,
glistened in the light from an east-west border check point. A sedan
rolled up, its tires singing on the wet pavement.
Clearly, imagined situations were OK with the editorial board. Perhaps this was because of the $500 prize on offer for the best article, one of the two criteria being "literary qualities". Thus, it is possible that, not knowing the official name 'Operation Anthropoid', Jaggers simply made it up (as he did the dialogues, though these may also have come from or been inspired by conversations with Moravec - assuming Jaggers even met him). It is worth noting that some details on Operation Anthropoid were still classified until around 1995; if Jaggers was junior at the CIA, he may not have had access to such classified material.
Interestingly, Moravec does not reveal the name 'Operation Anthropoid' in his 1975 book (though he must have known it given his role in selecting and instructing Kubis and Gabcek).
