I wondered that too. Especially given how JNT went on to make so many references and call backs to the past in the next couple of seasons. And he apparently approached both Elizabeth Sladen and Louise Jameson to come back as the companion when Tom Baker regenerated. So having a previous companion appear wouldn't have been something not to be considered.
I assume the story was written as it was and it just so happened that Jacqueline Hill was cast. By that point changing the story so that she could play Barbara might have just been too much effort. If you're going to feature an old companion you'd need to reference it a bit and, from memory the abducted human part wasn't a very big role, so it may have needed to be developed more. And then you'd need a scene where the Doctor recognises Barbara and there's some explanation of regeneration, etc. I'm not sure what the time frame was in those days between casting and filming, but it probably wasn't enough for a rewrite of the script. But definitely a missed opportunity.
And, of course, that highlights the missed opportunities in the new series of getting both William Russell and Nicholas Courtney to appear. Coal Hill School as a major setting for series 8 offered an easy opportunity for Ian Chesterton to cameo (especially since he'd been confirmed to be on the Board of Directors). And even given his poor health, how hard would it have been to film a video call insert of the Brigadier in one of the many UNIT episodes?
