"Could everything be done at its proper time" -- is it a question?
No, it's not a question. You were right in noticing that the auxiliary verb could is placed before the subject everything. So as a standalone sentence, it would be a question. Questions have inverted subject-auxiliary order: "everything [SUBJECT] could [AUXILIARY] be done" - "could [AUXILIARY] everything [SUBJECT] be done?"
However, in your example it's not a question. Why? Because of the phrase only thus, which is a restrictive phrase. You see, after negative and restrictive phrases we can do subject-auxiliary inversion. This is done to provide emphasis. Hence, it's often done in literature.
Negative phrase "never":
I will never jump into the sea.
Never will I jump into the sea. (inversion: "will I jump into the sea" looks like a question, but it's not)
Restrictive phrase "Only for a million dollars":
I will jump into the sea only for a million dollars.
Only for a million dollars will I jump into the sea. (inversion: "I will jump" -> "will I jump")
I've added the tag "subject-auxiliary inversion" to your question, you can look up questions related to this topic.