I hadn't thought of this before but this just came to mind: why did Suho stop Bumseok from attacking the bully with the mic but he didn't stop Sieun from beating Yeong Bin with the book?

I get that Suho's whole philosophy about fighting is "don't cross the line" but what made those situations different?

I don't know if I would call them theories but I have some possible suggestions. 1. Suho actually witnessed the mounting bullying & teasing that Si Eun experienced so he felt the payback was fair and justified 2. Suho could tell Bumseok wanted to blungeon the bully (potenially killing  or seriously injuring him) and Suho didn't want to be a party to that especially since it had been Suho's idea to confront them in the first place. 3. Si Eun handled his bully/bullies by himself yet Bum Seok was reliant on Suho's presence which made Suho feel responsible for the situation.

Does anyone have any thoughts on this?

I am a bit late to the party. Anyhow, I have just watched the scene and I believe that it was a mix of your 2nd and 3rd point. Also, Suho and Sieun weren't friends when Sieun escalated so I guess he only intervened when it was close to reach a point of no return. However, when Beomseok escalated, Suho and him were friends. Suho protects his friends so I guess he didn't want the line crossed. Additionally, Sieun kind of reacted within the moment of bullying, I guess, whereas they kind of set the situation up with Beomseok's bullies. There, Suho's responsibility would come in as well. Also, we should not forget that they did not seem to beat bullies up before the incident with Sieun and Yeong Bin, so maybe he did not want to make it a habit either.
Oh, and Beomseok already behaved weirdly, treating his friends badly and was an ass to anyone who did not agree with him or did something against his will. Even the perception thereof was enough to tick him off. So he was literally a ticking time bomb. And an ungrateful selfish prick who sees himself as a victim even in moments that he is not. 

Also, as we see right after, he is a weakling that beats people when they are already kneeing or laying on the floor. Bully behaviour.

(Ngl, I am sure if he had a girlfriend and she would accidentally say the wrong thing or would have talked to another guy that Beomseok did not approve of, I could see him get violent with her as well).