playing barre chords with your thumb in no way risks injury, nor does it prevent you from playing them the correct way when the situation arises!
there is no wrong or right way to play guitar, christ.
It
can actually injure your hand. Well, unless you have huge hands like Hendrix or Vai.
I particularly do not have huge hands, and I played with my thumb over the neck for a long time; I did chords with the thumb and all the shit, and since I played a lot, at some point I got tendinitis (or however you call it in english).
I was told by the doctor that it was probably because I wasn't playing right. This made me mad, so after some months, when my hand had healed, I started serious lessons of classical and electric guitar, and I must say that just then (after playing for about 3 years) I learned to play the guitar.
Just simple things like always pressing the strings with the very tip of your fingers, or keeping the thumb in the centre of the back of the neck can give you such versatility and agility in playing is insane.
I mean, I still use the thumb to make chords sometimes, but only when I am playing stuff by SRV or like John Lee Hooker, cus they have some thumb fretting techniques and stuff, but in general I never put my thumb in strings.
I would advice you that if you wanna take guitar seriously, learn first how to play properly with proper technique, and then once you have mastered the guitar well enough (you feel comfortable playing; it feels natural) move on to your own technique (what would feel even more comfortable).