Accusations were verbal, not physical abuse. They were fired right around the time Episode 5 of Season 2 was finished. The show went on a production hiatus at that time. I suspect they retooled the season arc heavily, making the decision to cast Ethan Peck as Spock (Spock was originally supposed to only appear as a child) and creating the whole Control arc rather than the spiritual/woo aspect that Berg and Harbets were originally going for. Likely CBS pulped the original arc so they no longer got story credit/didn't have to pay them.
It's a shame, because the original arc of S2 was shaping up to be REALLY good and intriguing. As jarring and off-balance as S2's second half change and finale ended up being....it's still quite amazing they managed to pull it all together given that they essentially scrapped an entire story and pivoted to another.
As much as that weird mid-stream change hurt S2, I still find it to be a stronger, more entertaining offering than S3 or 4.