@Zerio One of the reasons we chose General is because of who Kongming was in real life, rather than just because it was a replacement for -san. Cat lovers love to give their cats strange names, and I would say using an honorific like -san is about as strange as calling them General. Additionally, they don't always call her General Kongming -- they tend to just go with Kongming or the General as well!
We chose not to use honorifics for most circumstances in this light novel because they're mostly in a pseudo-European fantasy setting, where using honorifics would be quite odd. However, there are instances where we kept honorifics (such as "Mina-nee" for Minato) since it's only used by the Stewarts/Tanakas amongst each other - and in a setting like that, it would be normal to have honorifics. Since they introduce Kongming to other people in the pseudo-European setting as -san on occasion, we needed to find a way to make that balance out as well.
There are some plot related reasons later on that we chose to do it this way, so I hope you'll continue reading to find out what those are as well!