Just my 2 cents:
never listen to players! Gather stats, analyze them, and then make an informed decision as to what is the right way forward.
Players opinion can be part of your statistics, they might be all of the statistics you have / can collect / need to collect, but always take players opinion with a grain of salt. Players will try to skew your statistics just to get an advantage with a newer patch, or keep an existing advantage. Players interests are not your interests, and the vocal minority that is normally being heard is not speaking for the majority of your players most probably.
What does that mean in your case? That means that when players tell you your new mechanic sucks, and the old one should stay, they do not say that the old mechanic is inherently better or worse than the new one. They just state it seems to be better to them, as individuals, at the current point in time.
1. Maybe they loose an advantage they had before, some inbalance they were able to abuse
=> you can safely ignore their opinion for the sake of your games balance
2. Maybe the new mechanic is confusing to use, maybe players do not understand it
=> go back to the drawing board and see if the mechanic itself needs tweaking, if you need tutorials or better UI Feedback
3. Maybe the mechanic is changing the gameplay to such an extent that players might not like the game anymore
=> this is now a question were you need to ask yourself: is the new direction better for the game? is the amount of players you might loose because of it greater than the amount of players you might gain thanks to these changes?
In your case, Friendly fire will certainly cause the gameplay to get very different, and might confuse players because of lacking feedback and tutorials.
Make sure you really think about the impact this new mechanic will have on gameplay (can a unit hit itself? Will you give players UI Feedback when their units line of fires cross friendly units? Will you prevent units from shooting in this case to prevent hitting friendly units?)....
Make sure you update your Feedback (graphics, sounds, texts) to let people know when they risk friendly fire, or when they just hit their own unit. This will give players the options to avoid friendly fire, so that in the end friendly fire will still change gameplay somewhat (cannot form the firing line of units that happily fire through each other, and other similar tactics used in games without friendly fire), forcing players to adapt their tactics, while making it hard for players to accidently hit their own units.