Of course there is free will in the Matrix films- that is the point. Only the Merovingian is coming at it from a pre-ordained angle. If there was no free will there would be NO choices- whether you had already made them or not.
The only things being predicted are those things whose outcomes have ALREADY been decided by choices made. But there is free will and choice being exercised in the Matrix all the time.
The Oracle in EtM says that there are so many unknown factors that she cannot see what is to come- and what can these unknown things be, except what people chose to do? She even talks about how people will have to choose to help make the Path of the One.
Choice is endemic to the Matrix films as presented- do not let the Merovingian's 'bullshit' fool you.
I personally doubt this idea that the phone call in the original is after the two sequels. And I think that phone call being on the Architect's screen does indeed rule it out from being so, as the Architect was only predciting choice-created certainites (like the coming Trinity fight), and what was going to happen with the One was, again, NOT certain, as the Oracle in EtM makes clear.
Not impossible, but unlikely.