As we all know gods are the end game. If you get there first, you can easily wipe out you closest rivals and take server control.
Now that isn't all bad, as gods are the nuclear weapons of this game, the current issue is that lack of drawback outside of resource farming.
My go forward suggestion: Add a light and dark spirit (like corruption but incurable) When you kill players who are surrendering or use the god nuke, you gain massive amounts of dark spirit. This is applied clan wide and to anyone who joins the clan. Gods would then require different levels of dark light spirit in order to worship them, where you could be forced into a god that doesn't provide nukes, because you used gods to nuke too much or killed to many surrendering foes.
So for the players who like to pick on lower levels, they will eventually be forced into a god package that doesn't provide the clan greater Stregnth in defense or battle. If the use a god nuke, they may lose their god(s) and end up with hampered stats that will adversely effect them for the long term.
Where as destryoying a base/player of dark god, gains you light spirit. So you have a way to counter balance the spirit effects.
So essentially, players would get a performance benefit from destroying people would either kills players who where surrendering or destroying bases of the players who destroyed bases.
Basically, if you nuke a base, the rest of the server is incentivized to nuke you.