You're forgetting a fairly major issue here - Stapleton stands to directly benefit from Henry's death in a very public way, because in order to get his hands on the family money he has to out himself as a Baskerville. So that immediately gives him an obvious motive. What's more likely - a wealthy young extraverted aristocrat suddenly commits suicide and his money happens to go to a local relative, or his death was staged? The dog provides a far more plausible smokescreen than a staged suicide (when you consider that in those days, basically everyone accepted the existence of ghosts as a fact - indeed even in modern Britain it's not uncommon).