Oh yeah, Qui-gon should not be knowingly working in cooperation with the Sith. Though, following this idea, it could be revealed to him during the energy shield breather in the duel section of TPM. Conveniently, Obi-wan is out of earshot while Maul could conceivably let spill to Qui-gon the Sith's involvement, and his scheduled termination. This gives added focus and reason for Qui-gon to redouble his efforts to defeat him, and to plead with Obi-wan to go ahead with Anakin's training, which would lead, eventually, to the destruction of the Sith.
Interestingly, again in the EU, Grievous is made cybernetic with the help of a blood transfusion courtesy of Sifo Dyas! This in itself is...kinda lame, but maybe something in the same spirit could be transferred to Maul to keep his character relevant to the overall plot. At the same time, though, both characters are kinda unimportant to add additional and unnecessary convolution.