Find a new job, then give notice.
I've worked in this field since 1995 and am an employer at a fairly sizable team now and I'll tell you this is pretty close to industry standard. Competent employers do not have an expectation that they're going to get a heads-up before you start interviewing.
1987. My sister didn't know there was a root user on a Unix system. I found out she was interviewing after seeing her resume in her home directory.
We hired him. He was absolutely fantastic.
Or maybe because she had a problem I was in her directory and saw a suspicious file.
More than likely I was doing recon - I'm curious, so anything is possible.
Also I'm not sure how the existence of a root user plays a part because on the vast majority of unix systems the default home directory permissions are permissive read (this was true in 1987 and is still true now) and if your sister didn't know about root users it seems fairly unlikely that she knew about chmod.
If you are uncertain, and your current employment situation is feeding that uncertainty, it might be better to get out. I say this as someone who didn't really realize the way I was being effected by my work situation until I heard from a few people who left ahead of me.