Academia - innovative or repressive??

Around 1989, when I was studying my undergraduate Psychology degree, I asked a lecturer, "When am I going to be allowed to have an independent or exploratory thought (without being penalised)?".
Surprisingly honestly, he told me that, independent thought is not encouraged until you get to do your PhD.

So I told him, “Well therefore, by the time I get to do a PHD, I'll be so crushed and mind-controlled, that I won’t have any independent thoughts left."

He nodded silently. I suppose he wanted to keep his tenure.

Is that why academia can barely be trusted as a place for innovation?