I have read everywhere that the gold foil experiment performed by Rutherford was done hoping that the alpha particles face only a little deflection/no deflection however this doesn't sit right with me, the old model of Thomson clearly shows that atom is a positive sphere with electrons embedded in it, what made him think that positively charged alpha particles moving through this atom wont face a repulsive force from the positively charged cloud?
The Thomson or "plum pudding" model of the atom assumed a cloud of positive charge within which electrons orbited. In this model, the positive charge was so spread out that even if an alpha particle passed right through an atom, it would suffer only a very small deflection. The results of Rutherford's experiment showed that the positive charge and most of the mass of an atom is concentrated in a small volume (the atomic nucleus), leading to large deflection angles (which implies a large change in momentum) for the small proportion of the alpha particles that passed close to a nucleus. The proportion of alpha particles that were deflected through large angles allowed Rutherford to estimate the size of the nucleus in a model known as the Rutherford model of the atom.
Atoms are neutral, so the mean density of negative charge (mean charge per unit volume) due to the electrons would be the same as the density of positive charge due to the rest of the atom (an atom-sized sphere of positively charged matter in Thomson's theory). Therefore the mean repulsive force on the alpha particle from the foil would be zero.
Alpha particles were expected to penetrate the foil, but suffer many very small deflections due to close encounters with electrons. These deflections would be very small owing to the alpha particle's mass being thousands of times greater than the electron's mass.
This is an extended comment. The |Thomson model of the atom, called plumb pudding,
The plum pudding model of the atom, as envisioned by Thomson
The Thomson atom is a sphere of electric charge anchored in space by its mass. Thus the alpha particle will not bounce off the atom like a tennis ball hitting a basketball, but will pass right through if the atom's electric fields are weak enough to permit it. Thomson's model predicted that the electric fields in an atom are too weak to affect a passing alpha particle much, given how fast and heavy alpha particles are. Both the negative and positive charges within the Thomson atom are spread out over the atom's entire volume, and Rutherford had calculated that this volume was too large for strong deflection to happen.