Paragon, Smite, League of Legends, Overwatch, anything where fast paced team vs team combat is common changes in spell colours depending on which team you're on is common place. Just makes it really easy and simple to quickly identify if the spell on the ground is friendly or foe.
Not suggesting it would work as well here may alter the dynamic of PvP too much.
Other than a bit in Overwatch, an FPS shooter, and 2-3 spells in 13 mins of LoL gameplay I'm not really seeing much. There are multicolored spells all over the place. Including countless times i see red players shooting blue spells and vice versa.
I will note that you shouldn't be comparing 'common practice' across types. FPS, RTS, MOBA, MMO etc. are all very different in terms of what works and what doesn't.
In any case, ideas are never a bad thing. But in this case, I'll stick to my initial thought.