If I recall correctly, in FFE doing missions for one side would make you lose 50% of those points for the other side. So you could rank up with both navies but it would take twice as long. I think that would be a good thing to introduce.
You should probably be able to go negative also. Lets say you gain 200 points for the Federation, you're then -100 for the Empire.
Although, that negative number should be hidden.
Lets say you're 200 for the Federation, and -100 for the Empire. You then do an Empire mission worth 20 points. Because you're got a negative real rank, your standing only goes up by half.
So your Federation rank is then 190 (50% of -20 = -10), your real Empire rank goes up to -80 (+20) but your effective Empire rank goes up to 10 (50% of +20 = +10).
This will allow someone to rank up at half speed with a new navy, even if they've got a shocking record. But they must "pay back" that negative record before ranking up at normal speed.
In the above case, after the player does 200 points of Empire missions, they'll be ranked at 100 points for the Federation, and 100 points for the Empire. So they've done 400 points of missions but only got 200 points of credit total.
Like I said, because you're only losing 50% with the opposing navy, you could rank up with both sides, but it would take some time.