It was Earnest Rutherford and Paul Villard who first discovered the α-particle in 1899-1900. After some study Rutherford and scientist Thomas Royds, in 1907, proved that α-particle were Helium ions. In 1911, Rutherford performed his famous gold foil experiment. So yes, it was known that α-particle were Helium ions at the time of the aforesaid experiment.