That's a good question. The easy answer is no, don't worry about it. That said, there are a couple things you may want to consider...
How is your defense scored? If it is just TDs, sacks, and turnovers, then that will have almost no effect on your other players. They can both have success. However, if your league also gives/negates points for yardage and points allowed, you may want to look a little closer. If you think you have a great defense that will shut down your other players, you may want to consider backups on the offensive side. If you think your player is going to light up your defense, you may want to grab a different one.
It really is no different than any other week - you play the best player/defense based on the matchups. If your best matchups are Beanie Wells against the Giants and the Giants against the Cardinals, then that's what you play. Don't overthink it.
Also, it is similar to having a QB and a RB on the same team. You may feel like only one of them can have a good game. Actually, it doesn't typically happen that way, and even if it does, it is better than having a QB and RB on different teams and they both have dud weeks for you.
But again, of all the problems you'll have during the season, this one is probably at the bottom of your worry list.