I want to suggest a toggle in the weapon group menu that either unifies or separates different weapon types within a group.

If unified, they behave as now, all weapons in it will fire. If separated, the group will fire the weapons of one type only, and you have to select the group a second time to be able to fire the weapons of another type.
For example, you could put your two Sabot- and two Harpoon-launchers into group 2 and choose "separated". If you hit "2"in combat, you fire only the Sabots with every click (either "alternating" or "linked", that toggle also still applies). Once the enemy shield is down, you select the group again with "2" and now fire the Harpoons with every click.

The advantage should be obvious, it allows you to put weapons that you'd normally put in different groups into one group, freeing up groups to control other weapons more precisely.
A disadvantage of such a group is that you can't fire all weapons within it together, so you give up max firepower for finer control. E.g., it's nice to have kinetic and HE guns fire separately as long as you are in a flux contest, but once the enemy is overloaded and its armor broken, you might prefer pure dps from firing everything at once. That would not work well with a separated group.
I think it's really best for weapons you never want to fire together, like missiles with different damage types, or two very flux limited weapon types with different damage types.