I get that the feeling the writers didn't have the whole high-level story planned out and were making it up as they went along, one game at a time. So, we cannot infer what the Shivans were supposed to be, or what their motivations were, from the information in the games since the creators would not be able to answer these questions.
As a player, though, I felt that in the Freespace Universe there would probably be a very large number of species much more powerful than the Shivans controlling different galaxies. If the Shivans were only just a bit more advanced technologically than the Terrans or Vasudans, then it would not be likely that they controlled all the galaxies in the universe. They're more likely just the dominant species in our galaxy and a few others.
As for their nature, I get the feeling that the Shivan beings were creations, either by another race or they evolved/engineered themselves into 2 subspecies - one fully sentient and the other semi-sentient. The Shivans we interact with would be the semi-sentient ones, as they display some characteristics of machines and some characteristics of lower animals.
Regarding their motivations, I feel that the Shivan fully-sentient higher-order beings were not reacting to us at all, but were going about their own business. Their blowing up the Capella star was to create a jump node for their own expansion. The semi-sentient lower-order Shivans were probably reacting to us territorially, like animals or insects defending their space. They considered our stars to be their territory and did not consider it occupied, as we were not causing enough space-time disturbance to get noticed.