Kalista's Q shouldn't be able to proc her passive.
I honestly don't think this would be too much of a thing to ask for. The problem with her passive is that it isn't gated by cooldowns or mana. I think a fair change would be to make it so her spear can only proc her passive if she is within auto attack range when she throws it. This way, she would still be able to weave spear throws between her auto attacks, but it would gate her passive so she wouldn't be able to close the gap on an enemy she is chasing or allow her to jump over some walls quite as easily.