Holy Crap! I'm glad to hear somone had a good time with this merging of campaign systems.
I still think you can run SWA squads as baseline infantry in a military command heiarachy. This would do a lot to explain their funding structure and their need to lock down power sources (Isotopic fuel rods, Promethium, reactor pylons, etc, whatever...). Energy infrastruture would be a huge facet of hive warfare as forces move through that landscape, establish a front, and maintain communication & supply lines.
The gangs and to some extent inquisimunda warbands would function more autonomously and have a vested interest in local teritory holdings and income they could spend in diverse maketplaces.
That the two types of squads would invetably come into conflict, would be a simple narrative in any hive landscape. Much like the open ended sandbox that 40K was supposed to be.