I would assert that the author is using the phrase to clarify that he intends the expression, "a free thinker," to be understood is meant as a positive, or a compliment. So yes: indirectly it IS intended to be read in its literal sense.
There have been times throughout history where phrases like "free thinker," or "independent-minded," or "strong-willed" have carried additional subtext (meaning that is understood though not expressly stated), especially when used to describe women, slaves, foreigners, etc. (people that the speaker would have considered as "less" than themselves, either by virtue of their being the so-called "weaker sex", "savages", or "property").
By qualifying the statement with "in the noblest sense," the author is imparting said nobility either to the subject, or to his own feelings on the topic. In either case, he is making his position clear that he intends the words to be read as written, and is stressing that none of those secondary meanings are intended.
Side note: this is an excellent question. Not many people would have caught the nuance there, and of the few who did, most would have dismissed it. It shows you're really trying to grasp every part of the author's meaning. Well done.