I unfortunately don't have hills near where I live. Hills are great for exercise---mostly cardio but certainly they provide more resistance for your muscles than jogging on flat ground. If I had hills around, I would definitely make use of them. Plus, psychologically, I think it feels great to charge up a hill.
I don't think you have to worry about building too much muscle mass in your legs from runnng up hills, unless of course you want your legs to be really scrawny. If your legs were really scrawny (such as mine were when I was 16---I had almost no fat or muscle anywhere on my body), then running up hills would build up leg muscle. You would build up leg muscle up to the point that your workout required it. Passed that point, you wouldn't get bigger legs because your body wouldn't require additional muscle mass. If your leg muscles are already quite big, as you say, I don't think running up hills is going to make them bigger. Running up hills, in that case, is just going to be a great cardio workout, and if you've got hills around you, by all means, run up them as much as you want.
Why is it that you don't want even bigger legs? Is it just because you feel self-conscious about looking dispropotionate (which may not be as true as you think)? Or do you just want to be an endurance athlete and don't want a lot of extra muscle you don't need? Either way, I guess lower body weight training would be something you would have little reason to do. To be sure, I think most people (including myself) want stronger legs and should WT them more but maybe your goals are such that you have little reason to build them up anymore, in which case you are better off with long runs than squats.
