As I understood the second book's fluff. C. Hoffman blames the Arcanists for luring Ryle to Malifaux which led to his current state, which is fairly accurate, but he is unaware that Ramos is an Arcanist, so he has no ill will towards him, for now.
If anything, when C. Hoffman finds out the truth, the only change will be that he will go after Ramos along with the rest of the Arcanists.
Or are you thinking that C. Hoffman doesn't realize that it was simply them passing through the Breach that almost killed Ryle and he thinks that the Arcanists that just happen to show up at that time are responsible for Ryle's condition?
Either way, I'm not sure why he would side with the Arcanists.
Because Ramos 'saved' his brother? Maybe, but I could see how he would still blame Ramos for luring Ryle to Malifaux in the first place.
Finally, from C. Hoffman's fluff in the second book, he appears to have the demeanor of a good King's Subject that prefers law and following orders to an Arcanists-style rebellion. I got the impression that he would find it Improper to challenge a ruling authority in such a manner.