How would this be the case at all? I think all of Nutaku's events work that way: you use your stamina on the event or you use it on the story mode, nobody would be losing out on anything. It would be obvious new players are further behind or haven't completed certain stories we have because well.. they're new players lol.
I'm strongly in favor of adding something new to waste stamina on.. anything would fine. Ways to get girls, ways to get exp, items or even just more money. They need to add something in because at this point if you finish story, you literally can't use stamina on anything at all.