As you can notice nobody calls in Russian Francesco d'Assisi Франческо д'Ассизи - and I'm not saying this in ironical way. For instance, Leonardo da Vinci is indeed called `Леонардо да Винчи`. The thing is that traditions of transliterating names are not straightforward - some names are transliterated more or less at they "are", some names - do not. 

This holds true even for the name originally coming from the same languages. For instance, in Russian we refer French kings named Henri as `Генрих` though actually one rather can expect them to be named `Анри`. The same with `Карл` - who quite often were actually Charles. 

At the same time we have `Эркюль Пуаро`, not Геркулес Пуаро. Or `Артюр Рембо`, but not Артур Рембо. 

This is because names of some historical persons come for us through some other mediator language. In case of `Карл` and `Генрих` it obviously was German. 

In case of `Франциск` it was actually Latin - in Latin it's Franciscus - strictly speaking we don't know for sure how `ci` is supposed to be read in Latin. In fact, even in modern Italian to my knowledge there are some dialects where `c` in `ci` is pronounced rather as /t͡s/ than /tɕ/. There are different traditions of pronouncing Latin words - one of them to pronounce `сi` as /t͡si/ - and this is actually a German tradition of Latin pronunciation. Here's an excerpt from the Wikipedia [article][1] dedicated to this issue:

[![enter image description here][2]][2]

Historically German school of pronunciation of Latin words was widely adopted in Russia. This how San Francisco ended to be `Сан-Франциско` in Russian. It comes from that times when even Francis Drake who's now `Френсис Дрейк` was referred as:
[![enter image description here][3]][3]


  [1]: https://en.wikipedia.org/wiki/Latin_regional_pronunciation
  [2]: https://i.sstatic.net/XVw7H.png
  [3]: https://i.sstatic.net/NnSvs.png