I always considered the destruction of Capella as something the Shivans just did, weather be to harvest resources, as an environment to survive in (it could be they like it in there) or to scare off lesser species.
Also I don't think the Shivans want to wipe us out, atleast not anymore, perhaps killing the Lusifer and forging an allience with our bitter enemies (the Vasudans) intregued them? Or perhaps they only hate the vasudans due to being related to the Ancients (its hinted in the techs). That would explain why they were happy to take Bosh.
In the end we dont know, but its left us with lots of possibilities for storylines

Yeah, it looks like the Deimos and Moloch got taken out by EMP, then shattered by the oncoming wall of plasma.
Yes, because the EMP would be depicted as orange. Or there would be an EMP at all. Or it would cause the ships to rotate and drift like a physical shockwave. Or the EMP destroyed the planets!
There are many ways to interpret that scene but EMP isn't really one of them.
It definently wasnt an EMP, the orange wave was the sun's corona being blasted into space, incinerating anything in its path (hence the deimos and moloch being smashed up and floating wrecks) then the sun collapsed and sent a huge shockwave that just wiped out anything in the system.
Since people cant seem to agree what happens in the vid heres the vid:
http://www.youtube.com/watch?v=_qiWAgQeAVYTo me it looks like they've simply used subspace to cause a star to collapse, which is quite feasable.
And the red/orange wave IS the star's coraona being blasted out by the core collapsing, then the shockwave follows and finishes the job.