There were no torture scenes in the script, although I always got the feeling there was a plan to do more with March and Madison, the other main Genesis scientists, when they were named and cast.
Certainly, Nick Meyer did play with some of the action beyond what was written in the script, including shooting spontaneous scenes between Saavik and David Marcus to allude to a budding romance, and scenes between Saavik and Kirk to allude to an attraction. (I think I recall a recent "It's a Wrap!" auction mentioning extra unused Genesis personnel outfits being sold off; the novelization featured a cook, and McCoy had a line that Khan "even tortured the cook".)
There was definitely a variation of Chekov and Terrell approaching Khan's shelter - controversially, Meyer had a white stuntman painted black to portray Terrell rolling down a sandy slope after sighting Khan's child at a porthole, and the stunt section of that scene wasn't in the final script, only the child's face. Vonda did have the child in her novelization, but again, no mention of Terrell rolling down the slope.
Not used onscreen was a prop (or set dressing) of a painting, supposedly by Marla McGivers, which featured a portrait of Khan, Marla and child.
There was also an infamous publicity shot of a small child, dressed in rags, crawling around the Genesis device on Reliant's transporter pads. That sequence was dropped because it was decided (for the film's rating?) not to imply that there were toddlers on Reliant who were killed when the Genesis device detonated.