Nature will always find a balance, but the balance position may not always suit us.
Natural balance is not static: it is dynamic. In a given ecosystem, one species may gain the upper hand for a while, but then its predators will thrive as well because of the abundance of food. If they are too efficient, the predator may reduce the prey species so far that they themselves suffer a dearth and a severe reduction in numbers, which creates a window for the return of the prey species. Unless some other factor intervenes - such as the inadvertent introduction of a new predator, or a novel chemical, into the ecosystem - this dynamic balance will persist indefinitely.
What humans do is mess with the ecosystem on many levels simultaneously, resulting in a complex set of interactions that cannot fully be anticipated or understood.
That is the single reason why I think GM is the most dangerous technology of all: not that it is necessarily toxic - although it may well be - not that it is in the hands of powerful, profit hungry psychopaths - although it is, and we should be very concerned about that - but that NOBODY understands or can possibly predict the potential ramifications of interfering with natural process at that level or on that scale.