Even what he's saying could just be a manner of speaking. The meaning is still that the "Will of the Force" is being communicated through the Midichlorians. I don't think he really sees them as being sentient middlemen that re-explain what the Force is trying to say.

And as far as nothing contradicting what he's saying, he believes the Midichlorians are responsible for creating Anakin, and in ROTS, Palpatine says that the Sith had figured out how to manipulate the Midichlorians to create life. The implication being that it's possible that he or his former master has caused Anakin to be (a point that Palpatine actually brought up to Anakin in one of the script revisions). So right there is some ambiguity that directly contradicts Qui-Gon's take on things.