Its not like they'd necessarily make Afghanistan worse. Just more organized. Same chopping off of hands and religious oppression, but without constant terrorism-related deaths. And we'd also probably have a Baluchistan.
Nah, it'd probably be a disaster, both for Iran and Afghanistan. Iran charging into Afghanistan wouldn't even have managed what the American invasion did, and would have had difficulty matching the Soviets. Other things would have probably happened similarly - for instance, we probably wouldn't be talking about sanctions due to an Iranian nuclear programme, but rather due to Iranian unwarranted and aggressive invasions of a neighboring state. Though, I do agree that it couldn't have made things much worse for Afghanistan; Afghanistan never really left a state of civil war and internecine tribal feuding since the Soviet invasion. Ironically, it might have justified continuing American support of the Taliban in order to tie down the Iranians, though, and definitely would have encouraged ongoing Pakistani support. In the Iran-Iraq War, the Soviets may have been Hussein's biggest suppliers, but American allies were more than willing with a wink and a nod from Washington to support Hussein against Iran as well.
I also strongly doubt there'd be an independent Baluchistan, unless Iran lost. The vast majority of Baluchi people are in Iran or Pakistan, not Afghanistan; Iran wouldn't want an independent Baluchi country any more than they would want an independent Kurdish country. While it would weaken their enemies, it would also weaken themselves.