Due to the Hugenotten influence (from 1685 onwards) in Berlin and Prussia (there is no such thing as a 'Prussian' language) , the French language and culture (unaffected by Napoleons 'visit', as you term it, and the war of 1870/71) were very strong to the end of the 19th century.
As apposed to other countries (where only the aristocrats spoke French), in Prussia it was spoken by part of the population in everyday life.
The Berlin dialect today is still strongly influenced by French.
It is unlikely that anybody saw the need to rename an existing Merit for the reasons that the OP gave (assuming anyone wanted to change it at all).
The Pour le mérite für Wissenschaften und Künste is an Ehrenzeichen and not a Verdienstorden.
Reasons for not renaming the Order of Merit
One of the more obvious reasons is, that the french text is incorperated to the metal itsself:
- Prussian Military Pour le Mérite
(Order For Merit)
- with oak leaves (Eichenlaub)
The emblem of King Frederick II of Prussia, who established the honour in 1740, is also incorperated into the metal.
Since the King was still greatly respected, to change his original intentions of what the honour stood for, simply because of the french text, is unlikely.
If anti-French sediment was so great after the Napoleonic wars, then why didn't they give the newly created civilian version in 1842, long after 'anti-French thing' (as the OP call it), another name?
The present association, in its PDF about the history of the order (Pour le Mérite – Über die Sichtbarmachung von Verdiensten), does not meantion any attempt to change the name. Nor any meantion that there was any opposition to using a French based name. It only states that the Nazi's (in 1934) wanted to to get rid of the association that issued the civilian order, not to rename it.
The only 'hint' that we have here is that no Pour le Mérite were issued (neither civilian or military) between 1934 and its reintroduction in 1952.
The OP quotes the Wikipedia citement of the 1899 Cabinet order, which aims at the replacement of foreign words with German expressions, as a foundation for his assumption that this would/should apply also to French based names of objects.
Had this been the case, they would have done it then. But they didn't.
Between 1914 and 1918 the medal was awarded 687 times and the oak leaves for the Pour le Mérite 122 times.
The Hugenotts, who had no reason to love France (royalist or revolutionary) but nevertheless retained their French identity, were respected and influential in Prussia. It is therefore doubtful that they would have supported such a general renaming of existing names or objects solely because it was based on french.
If this was truly the case, then Pommes frites (which the Hugenotts may have brought with them when they sought refuge in Prussia in the late 1680's) should have suffered the same fate as French fries did in 2003 where they were renamed to Freedom fries (just as the suggested renaming of Sauerkraut to Liberty Cabbage in 1918) in the United States. But it didn't happen.
These aspects of the background are completely missing in the OP question, making the background information too one sided. It gives the impression that the OP is only interested in answers that agree with his pre-drawn conclusions.
For these reasons I casted the second vote to close this question as Opion-based.
- Hugenotten in Berlin – Wikipedia (German)
- Pour le Mérite – Wikipedia (German)
- Pommes frites – Wikipedia