Rutherford experiment, involves the collision of the positively charged helium ion moving with kinetic energy. The effect on the subatomic particles depends on the positive charge and the kinetic energy of the helium ion.
In air or other gaseous medium, the medium will give resistance to the movement of the helium ion, and reduce their kinetic energy. In addition, helium ions, because of their positive nature may collide with the gaseous particles, ionize them and may not reach the gold foil at all.
So, maintaining a vacuum in the chamber is essential for the helium ion to hit the gold foil.