Question: So, I'm playing this video game and I came across this sentence that uses "stem from" in an alien way to me.

"Their zeal is admirable, but their ideas impractical for a society that must maintain secrecy and organization **to stem** its own genocide **from** coming about."

I know that "stem from" means Originate from:(TFD source below)

stem from (something)
To come, result, or develop from something else.
My fear of the water stems from the time my brother nearly drowned me when we were playing in our cousin's pool as kids.

But this usage is different. It is as if it means "to prevent". There is one definition on TFD that sort of fits but it would have to be an abbreviated version of it.
(TFD def)
**stem the tide or stem the flow**
COMMON If you stem the tide or stem the flow of something bad which is happening to a large degree, you start to control and stop it. *The authorities seem powerless to stem the rising tide of violence. The cut in interest rates has done nothing to stem the flow of job losses.*

is it possible it is that meaning?

Answer: 
The simple past ("was") is used to discuss possibilities. The past perfect ("had been") is used to discuss counterfactuals. That is, if you're uncertain about whether something happened, and want to discuss the consequences of it being the case, the simple past is appropriate. For instance, "If it was raining, they will be late". If you know something didn't happen, but want to discuss a hypothetical world in which it did happen, the past perfect is correct.
One does not say, "If it was..", but "If it were..." This is the subjunctive mood, used in stating a condition *known* to be false.

[Tevye is grammatically correct](https://genius.com/Topol-if-i-were-a-rich-man-lyrics) asking, "If I were a rich man."