After some more reading it was said that:

It appears to be caused on shared webhosting servers. Infected accounts gain access to change other users files. Doing so changes the ownership of the file to the infected user's account name.

One Solution is to chmod the index.php to 444

I also tried redirecting the domain to another file, the page doesnt even open even if it still gets infected after that.

After reading again, it seems that is what other people are doing too to deal with this problem.

Atleast I have a clear name for it now, I believe this malicious crap is called iframe injection