In this particular game, birds ARE dragons. If memory serves me right, most dragons are "hybrids between the ancient dragons and other species" - so technically I guess you could say very few dragons are pureblooded, and this shows in their various shapes, but they are certainly considered dragons.
If you do not wish to fight them, then you can do your best to avoid that, but Rii has a very valid point - it would be extremely awkward if we were able to tame 'gods' and the legendary dragons. They are very prideful, and have their own responsibilities. Even the 'god skills' which we can earn at level 60 can not be considered making you a god, nor having tamed a god - its the dragon gods lending you their strength.
When you hurt the dragons, such as Sardok, you are simply knocking some sense into him; waking him up from Fedranas manipulation. As for why Fedrana is manipulative, she was banished by the legendary dragons in the past and is seeking her revenge. If we think of what this represents, it could be that in all species, and in life there will always be both good and bad (and im starting to sound like an english teacher reading too much into things), or they just needed some bad guys to the mix.