I'd say one of the biggest things is to try as much as possible to always make the all-around chute experience as pleasant for them as you reasonably can. If possible, do as much work as you can in the lane, and don't even put them into the chute unless you need to for something more. Beyond that, avoid use of hot shots, no yelling, keep ALL WORKERS CALM, AND... maintain calm, quiet, gentle chute operation and functioning.
Auto headgates with the cafe' doors are notorious for the animals ramming into them hard and slamming them shut... BANG-CLANG... bruised shoulders, then jerk hard back to try to escape, then jump around because you're caught, etc. Then because you often can't "release" without manipulating the animal first (smacking them on the head/or forcing them forward some), you generate more stress. Would YOU want to go back into that thing after that kind of an experience?
A straight in/out functioning headgate operates much more quietly (AQ, Priefert, Lakeside, etc.), and doesn't HAVE to be a torture clamp device on them. The Priefert headgate will operate on auto without the "slam"... doesn't need to be (and SHOULDN'T BE) squeezed "tight"... it's DESIGNED to gently take up the slack without squeezing her neck unnecessarily as long as it is lubed up right. Hydraulic headgates often are pressed too tightly by the operators. Hand operated ones more often than not get squeezed too tight too... I see operators all the time cranking on that handle to where they can't apply any more pressure without another man... thinking that they'll escape somehow otherwise... or they think they'll somehow "control" the animal better if clamped really tight??? Maybe they think they'll be able to teach that sucker a lesson if she won't stand still... IDK.... IMO, that just makes them fight more.... = more stress, = more resistance to ever putting their head through/into that thing again.
If the animal is balking because she's seeing a man ahead of her outside of the chute, then the man is in the wrong position, and simply moving relative to her coming in (so that she feels she can "escape" past you) would likely solve that... but if you're stuck at the front because you HAVE TO BE to run that headgate handle, you might need to come up with a solution for that. The AQ sliding handle is helpful for that... Priefert auto-catch works good too... as do hydraulically run headgates, if you can afford it.