I have an RP like the one you described. My flag trader, Benjamin Epstein, is the great-uncle and grandfather of not one but two ex-commanders of the 101st; half-Maltese, he ran a lucrative Cardamine-smuggling operation for 45 years and donated most of the profits back to the Maltese military, which he also flew with for a short period of time in his youth. Now he has bought his retirement ship - the former OSC Flagship, a custom Royal Liner, which was repossessed and put up for auction because the tourism market tanked and OSC couldn't pay its bills. Chaos ensues. He now runs (mostly) legitimate (mostly) human cargo after 50 years of dedicated service - and he expects not to be bloody pirated, particularly since most of his profits are still donated (both in-RP and out) to the Maltese military. Any Outcast who hits him up gets a talking to. Any Outcast who persists gets a much sterner talking to, possibly involving event horizons.
And you're telling me there's something wrong with that, that two years of RP right there? If a player expects to not to be pirated because they lead a faction that's crap, but if a character expects not to be pirated because of who he (the character) is then people ought to respect that RP if it pertains to them.
That RP is dangerously close to power-gaming, if not power-gaming already. (Apologies, but yes.)