Manchild,
You stated that the airplane you fly is "weight critical." What did you mean? Are you extremely performance limited at higher weights? Or is the empty weight just heavy with little pay load after fuel?
You do what you can accept, but know this. You start accepting little things, then bigger things. Nobody ever starts out being willing to accept or do the big things...but once you start down that path for an employer, the employer just wants to keep taking, and taking.
Safety of flight issues are supposed to be untouchable things. Most places, invoke the holy phrase "safety of flight," and the world stops spinning and comes to a screaching halt. But only if you stand up for it.
As a junior employee, this is difficult. You sometimes have the option to shut up and do it, or quit. I've quit before, rather than put up with what I found unacceptable.
The question then comes back to you. What do you find acceptable?
If the aircraft is range limited, then it needs to make fuel stops. If the aircraft is being pushed so far that it needs that extra two hundred pounds of fuel, it's probably being pushed too far. This is the thing you can see happening in your department. What about the things you can't see? How many inspections or cycles over are certain components? If they're willing to let one thing go, what about others? Is your mission so important that pushing fuel or other limitations becomes necessary every time? If not, then why are they doing it?
These are things you need to ask yourself when you consider what you can live with and what you cannot, what you can accept, and what you must reject.
Operationally, I'd much rather have extra fuel at the end of the trip than too little. How you accomplish that and what you're willing to do to make it happen is up to you.