I am not sure which factor was prevalent. At`the time when I lived there, catholicism was strongly promoted by Houphouet Boigny, who had a copy of Rome's st Peter's cathedral built in his native city, Yamoussoukro, allegedly funded by his personal fortune. But there was no kind of persecution against Muslims. Furthermore, both religions had been adapted by the locals and were mixed with animist practises.

Nonetheless, ethic roots have always been a strong identification factor in Sub-Saharan Africa. Colonialists created artificial borders defined with straight edges without taking into account resulting the ethnic divisions that resulted from drawing a border with a ruler.
To sum up, my personal view is that ethnic divisions were the main driving force.

When through hell, just keep going. W. Churchill

When it comes to amplification from the outside,I cannot but think of the wishywashy, stop-and-go attitude of the French government (cf the Marcoussis peace summit held in Paris and its consequences).  
Unlike Great Britain, France never resolved to admitting that maintaining a colonial empire was more trouble than it was worth, nor did they succeed to dismantle the colonial machine even in the countries that were long independent.

When through hell, just keep going. W. Churchill

According to official figures, Muslims make up a rough 40% of the population, with Christians not far off at 35%, the balance being made up (personal guess only) by animists.
There are 60 ethnic groups in the country, the Baoule being dominant. Former President Houphouet was a Baoule, but he was wise enough never to capitalise on his ethnic belonging to justify his leading the country. He always portrayed himself as a federating figure. I remember one of his quotes regularly opening the evening TV news : "peace is not a word, it is about behaviour"  "la paix ce n'est pas un mot, c'est un comportement".

When through hell, just keep going. W. Churchill