It is widely understood within the coaching community that that having your athletes develop general physical fitness is the primary way to avoid injury when participating in their specific event or sport. Since Aikido itself has few physical fitness benefits compared to a even a basic strength and conditioning program, I am of the opinion that general physical preparation (gpp) should be undertaken as a co-requisite of Aikido, if only to mitigate some of Aikido's injury potential.
Benjamin, well said. I don't think aikido is entirely alone in this among the martial arts, but it's maybe further along the scale: it's one of those activities that require
good conditioning (in order to practice safely and effectively) much more so than they develop
said conditioning. Alpine skiing is another good example: the demand on the muscles comes immediately, the building of muscular strength lags behind, which is why you get a lot of once-a-season skier injuries. If you ski, or practice aikido, or any of these activities, and you manage to stay injury-free, eventually you will develop decent conditioning...but it's not the safest or most effective way to get there.