When you click on a stack after selecting a strategic spell, a box pops up with the individual units in the stack and boxes below them.
left-clicking selects a unit
right-clicking inverts selection
a Done button will cast the spells.
This is the system used in the Age of Wonders series, it worked perfectly well there, and I see no particular reason to re-invent the wheel. This would probably take someone a day or two of work, but would solve the problem entirely.
