According to the original definition of "philosopher" in the Oxford English Dictionary, it less meant "magician" and more meant "sage". Or "wizard", in its original sense. That is, a wise old man, particularly one connected with the (not very scientific) ancient or Medieval sciences. A person who seeks out the truth.

It also had a connotation of "alchemist" which was sort of the same thing, in the same way that science and pseudo-science are connected--but a lot of "science" back then was also pseudo-science so the line is a bit blurry.

It's this connection where the term "Philosopher's Stone" actually comes from. "Philosopher" in that sense doesn't mean "magician". A "philosopher's stone" was a specific legendary object, like the holy grail or the fountain of youth. It was an object that was "supposed by alchemists to change baser metals [like lead] into gold or silver," according to the OED. Its discovery and development was at the center of the alchemy tradition for many centuries, though no real success was ever made in making the "philosopher's stone" a reality.

In the literary world, the "philospher's stone" often does exist, just like the fountain of youth does, and it is often portrayed as a magical stone that can change one thing into another, or even create things out of thin air.

But the term "philosopher's stone" also developed as a shorthand for con artistry, in the same way people later on began to talk about "patent medicines" and "traveling medicine shows".

Anyway, that went a little off topic, but together with the OED definition, and the explanation of the Ursus character in The Man Who Laughs' original New York Times review, and the time frame the film is supposed to take place during, I think it's safe to say that the filmmakers are using "philosopher" in the sense of "wizard" or "a wise old man of the Medieval sciences".

EDIT: I guess that's not too far off of the popular notion of what a "magician" is, but "magician" and "wizard" mean slightly different things. "Magician" can also mean a guy who performs in Vegas, and is intentionally deceitful, whereas a "wizard" is more of a mystic whose methods aren't necessarily deceitful, though they are obscure.

One more source.