It would be great (although I doubt that Capcom would think about something as complex) if that was a little hint at some kind of character development. Jill certainly isn't the same person anymore since what Wesker did to her (no one would be), and Chris has changed too. Maybe they just don't get along anymore, and some future game will be about them trying to re-establish their friendship while fighting zombies.
Judging by his obsession with finding her in RE 5, by the looks he gave her when she was rescued and by all the events they've gone through together your suggestion is highly doubtful. I dont't think that they have any problems in their friendship and I dont't think that Capcom thought that far.
I really start to believe that they are just not sure about Jill's role yet or they plan the next game with her in it and just want to keep her fans in suspense and increase the tension.
Agreed. I had the same impression as well.I figured they only mentioned Claire to link Sherry and Chris together