evidently, we're dealing with a coherence problem here. As you point out, reference is lost here.
I think it refers to "the use of force and violence to attain our goals"

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After reading the excerpt, I believe the "lo" refers to is "establecer un diagnóstico y un tratamiento eficaz". From what I gather this phrase is used figuratively rather than literally, as the article you're translating is about certain social issues. This seems to be the desirable end to attain. Here is my quick attempt at translating it:

If we know what happens/occurs, we will be able to set a diagnosis and [prescribe] an efficacious treatment. It is about substituting/replacing the use of force and oppression WITH* scientific knowledge of specific instances of violence and conflict. The ideas, the defense of own interests/self-interest, the identities and the** quest for solutions to social and political issues do not constitute a problem; the problem is always the use of force and violence to achieve that.

Notes:
* I would use "to replace/substitute X with Y" (where Y replaces X) rather than "to substitute X for Y" (where X replaces Y)
**I use the definite article "the" here because it sounds like the author has already talked about those factors throughout the entire article.

I hope this helps!

I wouldn’t necessarily tie the use of force and violence mentioned in the last sentence to a specific goal mentioned elsewhere in the text. The word SIEMPRE in “el problema SIEMPRE es…” points me in the direction of generalization applicable to ANY context, not necessarily the one we’re translating now.
Hence the indefinite articles: (use of force and violence) as a means to an end.