There are few things which needs to be taken under consideration before we come to any conclusion in regards to this query:
1. The sensitivity of the name which we have today was not prevalent and current at that time. Moreover, the name is name and the person and the character behind a particular name could be bad and not the name by itself.
2. Abu Bakr is Kunyah and not name in Arabic culture. We need to differentiate between names and Kunyah.
3. Few reports mention that names such as Uthman was used for Imam's son behind the name of the great companion Uthman b Maz'un and not the third caliph.
4. Well, the entire discussion shouldn't lead one to think that there was no dispute among the caliphs and Imam Ali (as). Its obvious that Imam Ali (as) had some strong criticism on how the Muslim Ummah was guided in the time of the 3 caliphs and Imam did raise his voice in a form of constructive criticism.
All the above mentioned point COLLECTIVELY make a sound argument.