To the Elder Gods, humans are are indeed vermin and pests. Annoying but insignificant critters who every now and again get sufficiently numerous or intrusive that they need to be swatted.
And while some of the older established human gods appear to be able to deal with the Elder Gods as...poor and embarrassing 'shirt-tail relatives', perhaps, but folks who have to be treated with a modicum of politesse at any rate...we New Gods are likewise vermin and pests. As deities, it's hard to swat us directly, but if we annoy the Elder Gods enough, our *followers* can certainly be obliterated with little effort.
Which doesn't mean New Gods and their followers are the helpless prey of the Elder Races and the Elder Gods. I expect reasonably trustworthy treaties/alliances could be made with several of the Elders, if the New Gods or their human (ugh) followers have something of value to offer.
Or, the New Gods can take the role of *successful* vermin, which is to say "try to get your business done without getting noticed by those with the power to squash you". Engaging in a long and obvious siege or smiting the offending Salamanders via a series of obviously-divine disasters would be a bad plan. Afflicting them with a nasty but seemingly-natural disease, or obliterating them out of the blue so fast that they don't have time to pray effectively for aid from the aforementioned Elder God (who, let's face it, can't *hear* every little prayer of their several million followers and thus might not even *notice* that a remote town of a few hundred souls has vanished...not for a few days or weeks, anyway....) But there's likely to be a BIG price to pay if it turns out that the town in question was of some particular import to the Elder God, or s/he just *happened* to be looking that way when the vengeance came down....
To do that last one right, you need to be able to think like a rat or a cockroach or a mosquito, and get rid of this idea that the PC is an OMGALLPOWERFULDEITYLOOKUPONMEANDTREMBLE. Which might be tricky given the premise of the game....