The Scored 5000 medal really wasn't well thought-out. It is impossible to obtain through normal play, as you only get 1 point per each bubble popped, and there are only 20 stages, after which the game abruptly ends. And you will end up with 3000 something points doing it that way. I know. Been there, done that. Even the game's own author appears to have only scored around 3000ish. The medal requirements should have been 3000, rather than 5000, points. OR the game should have been endless and not end abruptly on stage 20.
So how to get that Scored 5000 points medal then? At any point before you have completed a stage, right click and choose Forward then right click and choose Back. The stage will reset but you will retain your score. Repeat until you have greater than 5000 points. Get a ridiculously high score if you want but there's not much point beyond unlocking the medal.
Just be sure you do not game over at any point, as well as do not pass stage 20. (Yes on the glitched screen after right click forward it will say Game Over but it is not a game over. Ignore that. Just don't get a game over in play). Very easy to do by the way, as you get careless grinding out the 5000.
As far as I can tell this is the only way to do it, and seeing as how only myself and one other person (as of time of writing this review) have the medal, you're really going to have to take my word on that.
Hope it helps!