We can assume that drugs work on Magical Girls (at least to an extent) given that Octavia and Grimgrave get drunk in 3.3. It has also been heavily implied that the magic used by Magical Girls is affected by their mental state.
With that in mind, I think hallucinogens would make pretty good anti-Magical-Girl weapons. A gas would be best, but not all hallucinogens work well as gasses and you’d run the risk of friendly fire. Flechettes, darts, arrows and bolts all have the issue of a Magical Girls extreme reaction speed, but you could always just try more of them.
Some other fun options include: LRADs and other sound based weapons; LED incapacitators, Dazzlers and whatever the hell is going on with the “DIY Eyesight Deleter” (remember when working with high power light to wear the appropriate protection).
You could also try the basic pepper spray and taser although the lack of pained screaming during the fight in 3.6 indicates that transformation grants some degree of pain resistance (Signal also corroborates this while telling Octavia why she shouldn’t immediately run back to England iirc) But pepper spray and tear gas don’t need to hurt to greatly inhibit vision.
Hell maybe you could even get the US military to loan you an Active Denial System. It probably wouldn’t work, but it sounds cool as fuck.
