The Chicago Manual of Style is fine with that. "Insertions may be made in quoted material to clarify an ambiguity, to provide a missing word or letters, or to give the original foreign word or phrase where an English translation does not convey the exact sense." This is indicated with brackets.
That is exactly how I use them. When quoting critically, doing that makes a lot of sense. It can get confusing and be quite verbose without that particular device.
