Yes running average could be good enough for what you do; you can see PID as running average on steroid 
The other thing that you need to think about is if your stepper is not too coarse to drive the behavior you want? I don’t see the scale for your blue line in the sceeen capture above - seems that your flow undershoot with a very small change in the blue line and then there is tremendous inertia to go back down (is servo strong enough to block the flow?) -> how many ticks do you have between the low value and the blue peak ?