Niche protection is a good thing and I tend to highlight potential conflicts for my players as they advance. But it sounds like the rogue assumed he had the niche staked out by putting a token number of points into it.
I see this often in my game. One of the players tends to think that a +10 to the skill check is as high as he needs to go. When he was playing a rogue, this made for a very diversified rogue. But it also meant he wasn't very good at oppossed skill checks as the group increased in power. When other PCs started doing better with Spot, Listen and Search, he got a little twitchy. The problem is when PCs start running around at 12th level and the rogue expects his spot skill niche to be "protected" with his +10 total skill bonus, he really gave up that niche.
It sounds like the rogue in this case has done something similar with Diplomacy. He put some skill ranks into it to be good enough and then assumed that it was his niche. The fighter has been developing diplomacy and has finally exceeded the rogue. If it were really an important niche to the rogue, he could have developed it further and the fighter would never be able to touch him.
In this case, I probably would let it all sort itself out with the players. After all, the rogue still has a lot of utility in the group. As well, he has plenty of potential to use social skills in other situations. Perhaps the fighter brushes shoulders with the upper crust while the rogue gets on well with the common man. Or vice-versa. As a DM, I would look for those opportunities to bring more benefits to the entire group. They have two "face men" now and they can pick up information, friends and assistance from many different efforts.
Now if one or both players have serious issues with it, then it is time to discuss things. The fighter has really taken a hit in skills and stat boost to get where he is. He has been working at it. The rogue assumed that his high Cha and a couple of ranks would be enough to carry him through and then focused on other skills. If the rogue really wants that alpha male face man status, he has to work at it. Fortunately, he has 8 skill points base to work with at the next level. You want to be the face man? Put your skill points in the social skills.
But really, I see no reason why you can't have multiple avenues of working the general population with both PCs.