I'm not sure where you got the idea that excersize is discouraged for people with cf, in fact it's even more important to be active. Excersize, lift weights, run, swim, play sports, its good for you. The activity breaks up stuff in the lungs and increases lung function. Building muscle mass does the same as building fat. A fat person is never a "healthy" person even with cf. I have a 6 pack (or something close enough) and don't do any excersize per say, I stay active but don't do any specific weight training or running etc.
Talk to your dietican about it but I see no reason to not work out, in fact I've never heard of it being discouraged. Having the higher fat percentage is good and being a little bit "chunky" is good for a cfer, but if you can turn that fat into muscle it would be even better. Whatever you do, don't go on a diet to lose weight to get your fat levels low enough for defined muscles. That isn't how you build muscle whether or not you have cf. Talk to your dr and dietician and find a workout schedule that works for you till you have all the muscle definition you could ever want then keep at it, it's good for you.
But, all this being said; talk to your doctor first! A healthy person to should talk to their doctor before starting a workout regimine and certainly a cfer has additional concerns to doing so.
One more thing to add about this. If you really want to build muscles, it would be a whole lot easier if you are 100% compliant. Don't miss treatments. If you're noncompliant I can't imagine you having any luck with it. If you're not taking your enzymes, you'll have trouble getting enough nutrition to build any muscle. If you're off your antibiotics, your body will be too busy fighting infection to build muscle. If you're off your nebulized treatments your lungs will struggle to provide enough oxygen to your muscles. If you're neglecting your vitamins you will be in general messed up and incapable of building muscle. It all comes together with exersize and diet to create a healthy and strong person.