I think I get what you mean but I don't agree on all fronts.
1. that compounds derive from some difficult to handle gas is only a problem for the process chemists. In this case because the TFA-based precursor is available this is not a problem. Though technically, the production of that commercially available TFA will probably have involved F2.
2. Though indeed there are quite a few toxic compounds that incorporate fluorine, such as 5-fluoro-uracil, fluoroacetate etc this is not quite a general rule, as there are also plenty of non toxic medicines and materials that incorporate fluorine. It seems decently compatible with life compared, certainly compared to some other elements or classes of compounds generally.
3. specifically concerning nucleoside/-tide/-base analogs I wouldn't quite pin their cytotoxicity on fluorine, as a class these will tend to be toxic because they are similar enough to nucleosides to get where they need to be but dissimilar enough to cause problems and make systems that deal with nucleobase derivatives malfunction. Instead of 5-fluoro you can also put 5-iodo, 5-TFM, sulfur, alkynyl, etc there and get antiviral like, cytotoxic compounds
In any case, when it comes to this specific pfizer drug, I would say the presence of some fluorines is not a production problem and certainly not a toxicity red flag. For example, Derek Lowe, whose amusing post on some of the more dangerous fluorine chemistry you cite, also has the following to say about fluorine and medicinal chemistry:
"We med-chemists just love our fluorines - as long as we don't have to use, like, fluorine itself to make them - because they armor-plate parts of our molecules against being metabolized and can change the binding profiles of the parent structures like nothing else can."[0]
[0]https://www.science.org/content/blog-post/new-ways-fluorinat...