Can someone give me a brief overview on terminology here? I'm going with the assumption that PK is a Player Kill and Spike is going for big damage fast in order to get kills quickly without the target having chance to escape.
The issue mcmjon raises applies mostly, if not exclusively, to the smaller more open maps like Prison; Leviathan and Zikurat give players more options for demigod activity, and a weaker demigod might be able to avoid a higher levelled opponent in these environments. The thematic issue of the early lead culminating in late steamroller still applies though so I will offer some thoughts. My first thought was that proper character balance should partially eliminate this issue at its root, but looking at it further, with a smaller flag count (and thus the flags having a much higher effect) could it mean that one team can, as you say, develop such a large advantage over the opposing team so quickly? What is it that gives them that advantage in this example? The flags, the added EXP from PKing or the gold? Perhaps one or more of these factors could be toned down, although I am painfully aware that there needs to be enough incentive in killing other players to make people do it.
Some of the more "hardcore" on these boards may argue that an early advantage culminating in a late steamroller is just how it goes, but the way I see it, one of the most ignored parts of RTS design is the point where one team gains a significant advantage over the other team to the extent where the other team will not be able to recover. The problem is that there is no consideration into when this point occurs; it's fine if it's right at the end of the game, but in games like Sins of A Solar Empire that stretch into hours, it's a fun killer.
If you've got two teams of equally skilled players, I think a game of demigod could easily stretch out for quite a long time (although nowhere near as long as Sins, thank god), and I'd prefer there to not be a case where one team can take full control of the game within a few minutes of play. Assuming player skill is equal on both sides, play should be fluid, with the leader changing regularly.