Hi, JimJam! Please consider changing the title of your post to reflect the topic you would like to have an answer to. This way, Forum users will clearly understand what you are asking about and thus you can attract more users, who are able to help.
I would personally say that even if you have put a lot of points into some bonus that you no longer consider a viable choice, it is not a big deal, and you will eventually develop all the bonuses in the Great Hall. Especially on the early levels, there are no wrong choices. Unless you erroneously developed some modifier into a golden level of Medals, it would not drastically deteriorate your game experience. Though, I have to say that if you were able to do that, it won't be a big problem for you to fix anyway)