Halevi,
“The Sefer itself was for the most part rejected.”
Which part of the sefer are you referring to and rejected by whom?
There are many parts that do not even deal with Philosophy at all.
There is a saying from one of the great thinkers: for “one who had studied Shas and Poskim – its a ‘Morah’ – for one who didn’t then its a ‘Nevuchim”
As for recent Achronim , the Or Sameach and the Rogatchover constantly quote the Sefer haMorah..
iac:
“the language used by the RAMBAM was very difficult to translate and therefore yeshivos shied away from it.”
Kapach’s edition took care of that problem. And there are other editions with perushim as well.