Ruling on naming a mosque after a specific person

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.