TL;DR

Discovered my wife was cheating and she left me and my son to move in with her boyfriend.
I was planning on calling the "Youth Office" (Jugendamt) and report the abandonment which will basically strip her of the paternal rights and most probably give me full custody at the divorce. Now I'm having second doubts as I fear this will destroy her.

Story:

Two weeks ago I took a week of work and I didn't tell my wife to surprise her by picking her up from school: she came out holding hands with her boyfriend :)
At home, we had a discussion and thru some carefully asked questions I found out they've been seeing each other since January. What's more, she was skipping school (for which I payed) to "hang out" with the guy.

We have a 7 years old child and although I cried and pleaded her to remain, she chose to leave us and move in with him. She had an attempt to come back, but by that point I was too pissed (to put it lightly) and told her to go back to him.
Our son is taking this relatively well and I'm trying to keep him busy as much as possible (we're building a light saber, playing with LEGO etc).
Here in Germany there is an "Youth Office" (Jugendamt) and Monday I was planning on calling them and reporting my wife for abandonment. They will do an inquiry (mostly to confirm that she left and that I am a good father) but the result will probably be that she will loose some of her rights as a parent and my son will stay with me (at least until the divorce, but given the situation most probably after also).
Maybe worth noting that she never worked a day during our marriage and has no means of supporting herself, not to mention our son. I'm not doing this to prevent her from seeing our son - I promised her that she will be able to come see him whenever I'm home and available - but to make sure that at no point in time she will come and take him from me (even after divorce).
Now I'm having second doubts about this as I fear this will destroy her.