The cone is presumably only there to stop her scratching her eye so I think it should be fine to take it off for brief monitored periods. But I feel your pain with the eye drops, they can get considerable force behind a quick head jerk when they want to!
Done the burrito method so far but she is rather frantic
Anyway, took the cone off for a minute and it's a lot, lot easier with being to gently pull her head back.