I guess my only advice would be to use what feels right and put people's presumptuous comments aside. If you feel like you are learning and are inspired to build your game with whatever technology you pick up you are doing good.
More importantly, should I be focusing on making games with "pure" code, in other words building my own engine/physics? I'm torn here. I'm halfway through the game in Unity, but I'm not sure if it's what I want to be doing.
There is no right or wrong answer when it comes to what tool you should learn. If you're halfway through a game in unity finish it! Independent of platform and tools, It is awesome to be able to finish a game and say it's done.