No, I don't think distributing mega stones to all the Pokemon who need it is bad. If you're battling and one of your Pokemon faints before you can properly use it, it sucks for you. But, mega stones activate before any other action can happen so it could also be an unwise choice to. For me, I distribute my mega stones to all Pokemon that need it, but I only keep one for battle. Therefore, when I face a Pokemon I know I can beat, I mega it, and destroy my opponent.
So, you should give all Pokemon who need it mega stones, but I don't see any reason to have more than one in your party. Give the other Pokemon a different item that's useful such as focus band, plates, gems etc.
Hope I helped! Please like if helpful!