I've never felt the writers intended the Shivans to be conveyed as evil. It's hard to draw an analogy, the closest I can come up with is taking antibiotics to kill an infection. The bacteria causing an infection are alive, but no one loses any sleep over killing them. The Ancients, Terrans, and Vasudans might all be alive, just like bacteria, but as far as the Shivans are concerned, only they are worthy to live. There is no malice on the part of the Shivans, we're polluting the universe and the Shivans are there to clean it up.
As for Capella, I don't believe it needs nor should have an explanation. One of the key reasons why Freespace 2 has remained my favorite game over the years is due to the air of mystery. Whatever the Shivans' goals, they are beyond the understanding of mere gnats like us. The Shivans destroy. Why should always remain pure speculation.
Bosch is an interesting character and another reason why I enjoy the plot. The cutscenes humanize him and try to explain his motives. Its clear he's taken some evil steps along the way, but his intentions are noble: he wants to save his people from annihilation. When he first set out to form an alliance with the Shivans, he could not have known it would fail. No matter how slim the odds, Bosch likely considered it humanity's only hope for salvation. The war with the Shivans is almost certainly futile and some sort of accomodation will eventually have to be developed if the GTVA is to survive. The fact that the Shivans killed the crew of the Iceni is meaningless, they regularly slaughter entire planets. Maybe the crew was like cockroaches to be stepped on but Bosch surprised them by being intelligent enough to talk to them. Who knows? He might eventually work out a (Faustian?) bargain with the Shivans.