You've got a fun sentence there! Some guess work because there is no context, so I can't tell you 100%, but....
(Note: If you comment with some context and it leads me to a different answer I will edit as needed)
が fits just fine. It is basically saying that her remorse is crushing her.
Assuming you understand the first half of the sentence, which describes "自責の念", let's just focus on the second half. First off, I like simplifying sentences into the necessary pieces and putting them back together after I figure out the base meaning, which you seemed to be doing as well. You were right, the base volition of the sentence is contained in:
As an aside: the subject can skip over as many things as it likes. If you are having trouble, always look for the definitive subject of the entire sentence and the last verb, then build from there.
Anyway, this blockquote roughly translates to my summary above. Also, remember that 心身 means mind and body, that is important for getting the right image. So in the middle of that it says：
Let's translate this out of context of the sentence:
To find salvation in self-deprecation.
That bolded part is a prettly literal translation of "自らを貶める". So then all we need to ask is, "Who or what is self-deprecating?"
I think the answer is pretty clear by now, but just in case: the subject doing this action is Honoka, and the sentence is indirectly referencing that which is why it is hard to understand.
This is also where the guess work comes in to play: I'm guessing that Honoka found solace in being a guardian. Again, I can't know for sure since I don't know the context, but this is my guess. If that is the case, here is my translation:
Knowing that Honoka is abusing herself to escape the remorse, we can translate as below:
The remorse of being unable to do her duty as a guardian drove Honoka to find salvation in self-deprecation, and scarred her mind and body.
Edit for spelling errors.
Edit 2: I mistranslated a part, edited for correction. See comments for detail.