No, he wasn't.
Darwin certainly experimented with all sorts of crackpot treatments for his mysterious illness—and he was convinced that some of them worked—but even he drew the line at the nonsense that is homeopathy.
On 4th September, 1850, Darwin wrote to his cousin:
You speak about Homœopathy; which is a subject which makes me more wrath, even than does Clair-voyance: clairvoyance so transcends belief, that one's ordinary faculties are put out of question, but in Homœopathy common sense & common observation come into play, & both these must go to the Dogs, if the infinetesimal doses have any effect whatever.
I think we can safely take that as a 'no'.