Context. CH3CN (methyl cyanide) is one of the simplest and most abundant interstellar complex organic molecules (iCOMs), and has been detected in young solar analogues, shocked regions, protoplanetary discs, and comets. CH3CN can therefore be considered a key species to explore the chemical connections between the planet-forming disk phase and comets. However, for such comparison to be meaningful, kinetics data for the reactions leading to CH3CN formation and destruction must be updated. Aims. Here we focus on the destruction of methyl cyanide through collisions with He+. . We employed a combined experimental and theoretical methodology to obtain cross sections (CSs) and branching ratios (BRs) as a function of collision energy, from which we calculated reaction rate coefficients k(T) in the temperature range from 10 to 300 K. Methods. We measured CSs and BRs using a guided ion beam setup, and developed a theoretical treatment based on an analytical formulation of the potential energy surfaces (PESs) for the charge exchange process. The method employs a Landau Zener model to obtain reaction probabilities at crossings between the entrance and exit PESs, and an adiabatic centrifugal sudden approximation to calculate CSs and k(T), from subthermal to hyper-thermal regimes. Results. k(T) and experimental BRs differ from those predicted from widely used capture models. In particular, the rate coefficient at 10 K is estimated to be almost one order of magnitude smaller than what is reported in the KIDA database. In addition, the charge exchange is completely dissociative and the most abundant fragments are HCCN+/CCNH+ , HCNH+ and CH2+. Conclusions. Our results, combined with a revised chemical network for the formation of CH3CN, support the hypothesis that methyl cyanide in protoplanetary discs could be mostly the product of gas-phase processes rather than grain chemistry, as currently proposed. These findings are expected to have implications in the comparison of the abundance ratios of N-bearing molecules observed in discs with cometary abundance ratios.