I've been out of town for the past 10 days and my girlfriend slept over at my place while I was gone
Tomorrow I'm going back home, and I just got off the phone with her
She told me she's undecided whether she should sleep over at her place or mine
But if she sleep at my place again, she won't spend tomorrow night with me because she would feel awkard about spending so much time at my place
This is 100% a bullshit test as she wanted to see how I'd react if she won't sleep with me
I very calmly told her she can do whatever she feels is best for her
Until a while ago, I was very controlling in the relationship and because of this I was pushing her away
So now that I adopted this calm and relaxed attitude she sensed it, and angrily told me she doesn't like it (as in, why don't I put my foot down and tell her exactly what to do)

I'm really not sure how to threat her.She has a very low self esteem and I enjoy taking charge, but as I told you, it didn't work so well for me before.
Should I give her total freedom and let her decide what to do, or should I find a middle way between overly controlling and total freedom?

I'm pretty confused about this whole deal.

Take an educated guess.
Should I find a middle way between overly controlling and total freedom?
Voila.

What's the risk of giving her total freedom in doing whatever she likes

Sounds to me like you just swung too violently the other way. In a relationship, here's how I handle her reaction to you.

Tell her that you aren't trying to make her feel like you don't care, but that you see now that you were too controlling and just being an ass before and you didn't like how you were acting, so you've decided to make a change to improve yourself. This elevates you above a stupid game, makes you look confident in your ability to improve yourself, etc.

If she reacts negatively to a response that indicates your actions have everything to do with you being a better man, well then, I'd rethink if she was gf material.

She's aware I'm trying to change some stuff in my life and become a better man
Yet I don't fully understand if there's any risk of giving her total freedom or not

You have to slap this chick around.

First she whines that you show too much affection for her, control her too much into spending time with you. Then when you give her some freedom to make up her own mind about how badly she wants to stay with you, she goes all passive-agressive on you. Chicks like these are really the cancer of contemporary Western culture. Take that from a guy with two Master degrees and busy with a Ph.D in political philosophy.