I dont know. this seems as one sided as the luke vs neo bout. For this match to take place one or the other must be out of their respective element. If Trinity were out of her element, she would still, most likely retain her knowledge of fighting, but would, at best, only have speed equal to a professional athlete...,nothing more. In this case, Alice's super strength conquers Trinity's limited abilities.
If alice were to face off against Trinity in the matrix. She would still have her Speed, strength and knowledge of fighting. However, knowing better how to manipulate the Matrix. I would say Trinity wins. She too would have strength to Rival Alice and i have to assume her speed would be far above Alice's ability. Alice is obviously the superior competitor in this match because her skills are not bound to virtual reality. If she is given a respective amount of time to learn how to manipulate the matrix she may be in a league of her own, being bested only by Neo himself.