First off, “purifying” the hammer is probably not the right word for it, as the hammer certainly did not become anything pure or holy after bathing in the Fountain. Also, even more so than purity, the main characteristic of the Fountain is that it is the magical energy of existence. This same energy is what the Farang literally consume, so of course dipping a Fey bonded hammer in the Fountain would effect both of them. If anything, dropping a Mara hammer into the fountain would likely have the opposite effect that it did, destroying the hammer and leaving the Pseudo-Fountain a weird possibly corrupted mess.
Also, either from drinking its water or dipping the hammer into it (its unclear which since Berg didn’t enter combat between the two), Berg’s necrotic damage changed into psychic, which seems to have a very direct connection with the Farang and only happens when Berg’s wielding the Conduit.
In addition, it seems extremely likely that the power Tulpa consumed from the Pseudo-Fountain is what gave Tulpa the power to finally fully appear to Berg and create the Conduit in the first place, since Tulpa has said the Fountain’s energy makes him more powerful and has asked Berg to get more of it.
In conclusion, I’m still 99% sure there isn’t a Mara inside Berg. Only Tulpa, which may or may not be worse, depending on your philosophy. You can get rid of a Mara via magic, but the Farang are immune to it and invisible to heaven, so getting one off of your soul is probably tricky.