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Firstly:
With regard to it being makrooh to call Al-Madeenah Yathrib, it is narrated by al-Bukhaari (1871) and Muslim (1382) that Abu Hurayrah (may Allaah be pleased with him) said: The Messenger of Allaah (peace and blessings of Allaah be upon him) said: “They say Yathrib, but it is al-Madeenah.”
Al-Haafiz said in al-Fath: The words “They say Yathrib, but it is al-Madeenah” refer to the fact that some of the hypocrites were calling it Yathrib, but the name that suits it is Al-Madeenah. Some of the scholars understood from this that it is makrooh to call al-Madeenah Yathrib, and they said: What is mentioned in the Qur’aan is only quoting what some of the non-believers said. Ahmad narrated from al-Baraa’ ibn ‘Aazib that the Prophet (peace and blessings of Allaah be upon him) said: “Whoever calls al-Madeenah Yathrib, let him seek forgiveness from Allaah. It is Taabah, it is Taabah.”
‘Umar ibn Shabbah narrated from Abu Ayoob that the Messenger of Allaah (peace and blessings of Allaah be upon him) forbade calling al-Madeenah Yathrib.
Hence ‘Eesa ibn Dinar, one of the Maalikis, said: Whoever calls al-Madeenah Yathrib, it is recorded as a sin for him. The reason why it is makrooh is that the name Yathrib comes from tathreeb which means rebuke and blame, or from tharb which means corruption, both of which are repugnant meanings. The Prophet (peace and blessings of Allaah be upon him) liked good names, and he disliked repugnant names. End quote.
The hadeeth “Whoever calls al-Madeenah Yathrib, let him seek forgiveness from Allaah” was classed as da’eef (weak) by al-Albaani in Da’eef al-Jaami’ (5635).
Secondly:
It is makrooh to call a girl Yathrib for two reasons:
1 – It is a kind of imitating the hypocrites in their calling al-Madeenah by that name.
2 – The Prophet (peace and blessings of Allaah be upon him) did not like this name, and he changed it to al-Taabah or al-Madeenah, because the name Yathrib carries a negative meaning, as explained above, as it comes from a word meaning rebuke or corruption. One of the child’s rights over his father is that he should choose a good name for him.
Ibn al-Qayyim made some valuable comments on this topic, some of which we will quote here. He said:
It is proven that he (the Prophet (peace and blessings of Allaah be upon him)) changed the name of ‘Aasiyah (which means disobedient) and called her Jameelah (which means beautiful).
Abu Dawood said: The Prophet (peace and blessings of Allaah be upon him) changed the names of al-‘Aas (disobedient), ‘Uzayr, ‘Utillah and Shaytaan (devil). He called Harb (war) Silm (peace), and Shu’ab al-Dalaalah (branches of misguidance) he renamed Shu’ab al-Huda (branches of guidance), and he called Banu Maghwiyyah (lit. sons of the misguided) Banu Rashdah (lit. sons of the guided).”
Ibn al-Qayyim said: Names have an effect on the ones to whom they are given, and the things that are named have an effect on whether the names are good or bad, light or heavy, gentle or harsh.
The Prophet (peace and blessings of Allaah be upon him) liked good names… He told some people to milk a sheep, and one man got up to milk it. He said: “What is your name?” He said: “Murrah (bitter).” He said: “Sit down.” Another man stood up and he said: “What is your name?” He said: “I think it is Harb (war).” He said: “Sit down.” Another man stood up and he said: “What is your name?” He said: “Ya’eesh (long life).” He said: “Milk it.”
He disliked places that had bad names and he did not like to pass through them. During one of his campaigns he came to two mountains and asked what they were called. They said: Faadih (harsh exposure) and Mukhz (humiliation). He turned away from them and did not pass between them.
The Prophet (peace and blessings of Allaah be upon him) ordered them to choose good names and said that they would be called by those names on the Day of Resurrection. When the Prophet (peace and blessings of Allaah be upon him) came to al-Madeenah, it was called Yathrib and was not known by any other name, but he changed it to Teebah. End quote from Zaad al-Ma’aad (2/306).
To conclude: using the name Yathrib is makrooh, and we should use good names that convey good meanings.
See also question no. 1692.
And Allaah knows best.