So if the editorial decision were made to make the novels consistent with Countdown, there's no reason they couldn't be. After all, that comic sold very well, so there could be good marketing/economic reasons to tie into it. It would just be something that both the novels and STO chose to be consistent with, just as they're both consistent with canon. It would just fit into their respective tapestries in different ways.
It's worth noting that the STO history doesn't diverge overly from Treklit. The Needs of the Many
, for instance, cites pressure from the Gorns' various allies--the Romulans, Tzenkethi, Breen, Tholians, and Kinshaya, i.e. the other Typhon Pact polities in the main Treklitverse--as key in preventing an early outbreak of Gorn-Klingon war.
As for incorporating the events of Countdown
, well, what we glimpsed there is but the tip of the iceberg. How much did we really see of the broader astropolitical background?