Does the fact that I now know the answer to a question posed in the past deny the free will of the one who answered? For instance, my wife said yes to me when I proposed to her, does it therefore follow that she was not free to have said no? God of course knew the answer to the question before it was even formed in my mind.
Knowledge of an outcome and free will are not incompatible in the way that seems to be pre-supposed in the question. If man has free will then Mary has to have been able to say either yes or no to God, the fact that God knew that the answer would be yes does not actually alter that fact. If it did we would be no more than puppets and God would be responsible for all our actions.
For instance, if Mary is not responsible for the consequences of her yes then logically Adam and Eve are not responsible for the consequences of their actions either, in which case of course we implicitly make God is the originator of sin. Alternatively, if you choose to see a no from Mary as the ability to thwart God then logically you must also conclude that Adam and Eve thwarted God at the time of the fall.
The OP is essentially saying that he is not comfortable with man being responsible for the actions he takes freely. I cannot agree with such a position, God always knew we would fall and he always knew he would send His son to redeem us by the incarnation but humanity had a choice in it's fall and by God's grace a choice in it's salvation. It is fitting that Man should be required to make a choice in the process of salvation just as he made a choice at the fall, that choice is our second chance. Mary was the first to make the choice that we are all called to make, indeed her choice is a prototype of the choice we are called to make. She is the first Christian, our first and perhaps most important example of what it is to say yes to Christ, she is symbolic of the Church, just as her flesh became His body so now is the Church called to be His body.
To honour Mary ( and the glorified saints or even relics or icons for that matter ) is to recognise that God works through humanity to achieve Man's salvation, He does not make a mere legal declaration that we are not guilty, rather, through His grace He effects real spiritual and physical changes in the nature of Man and ultimately all creation.