What you have mentioned about the naming of mosques after specific people being makrooh is the opinion of some scholars, but the majority of scholars regarded that as permissible, not makrooh.
Imam al-Bukhaari said:
CHAPTER: Can it be said “The Mosque of Banu So and so”?, then he quoted the hadeeth of Ibn ‘Umar, that the Messenger of Allaah (peace and blessings of Allaah be upon him) organized a race for horses that had been made lean between al-Hafya’ and Thaniyat al-Wadaa’, and another race for horses that had not been made lean between al-Thaniyah and the mosque of Banu Ruzayq, and ‘Abd-Allaah ibn ‘Umar was among those who took part in the race.
Al-Haafiz ibn Hajar said in Fath al-Baari:
From this it may be understood that it is permissible to attribute a mosque to its builder or to those who worship in it. Similarly, it is permissible to attribute good deeds to those who do them. The author (Imam al-Bukhaari) put the heading of this chapter in the form of a question to indicate that there is a possibility that this attribution of the mosque to that tribe is something that was either known to the Prophet (peace and blessings of Allaah be upon him) and it happened during his lifetime, or it happened after he had died, but the former is more likely, and the majority are of the view that it is permissible. The one who disagreed with that is Ibraaheem al-Nakha’i, as Ibn Abi Shaybah narrated that he regarded it as makrooh to say “the mosque of Banu So and so” or “the musalla (prayer prayer) of Banu So and so,” because Allaah says (interpretation of the meaning): “And the mosques are for Allaah (Alone)” [al-Jinn 72:18]. His response was that the possessive in such cases is purpose of distinguishing it (from other mosques) and does not indicate ownership. End quote.
Ibn al-‘Arabi said in Ahkaam al-Qur’aan (4/277):
Although the mosques belong to Allaah by way of ownership and honouring, they may be attributed to others as a means of identification, so it may be said: The mosque of so and so. End quote.
Al-Nawawi said in al-Majmoo’ (2/208):
There is nothing wrong with saying The mosque of So and so, or The Mosque of Banu So and so, by way of identification. End quote.
Based on this, there is nothing wrong with calling a mosque by the name of a specific person such as the one who built it or prayed in it. Similarly there is nothing wrong with giving the name of a Muslim scholar or prominent Muslim figure to a mosque by way of identification only, but a mosque should not be given the name of someone who is known for bid’ah, because that is venerating him and encouraging the common folk to follow his way. And Allaah knows best.