Story points may have a ton of uses, but many of them are frivolous. Those that permanently powerup your character and have no other way to do it (use on s-mods, colonies; don't waste on historian when player can raid for blueprints instead) or those free in the long run (officers, run from fight, recover your ships) are the best uses. Thus, the execution of story points is that of currency, and no amount of embellishment will change that reality. Basically "You Require More Vespene Gas" trope.
Story points are infinite, so using them on temporary utility is not a "waste". If there was only a fixed amount of story points to get then yes, spending them on impermanent things would bad. But luckily, they aren't. Of course it's a currency - it's points you spend on things, there's no way for them not to be a currency.
But, like credits, it's a currency that is (until the level 15 crunch, which does exist if you don't go out of your way to farm in a way that is counter to intended gameplay) effectively infinite. Is spending a few thousand credits on a frigate tanker early in the game a "waste" because eventually you'll end up with a capital tanker? Of course not, you'll get more money eventually, just like you'll get more story points.