Hmmm ... not really.
When people choose a side at first, they don't know they'll be limited to specific options like sided Shadowbreed lines ; as i did myself, they will discover this long -long- after that choice (when they hit 200+ AND do mass pvp in war/tara).
Once they know it, then they reroll toons with knowledge. & the danger is that most people might go the side offering best strategic options BY NATURE ... wich could partly explain why there are twice more omnis than clan in TL7 on RK2 as i explain in OP !
In the end, you kinda justify this unbalancement on SB options by a roleplay point of view ? Honestly, that's a little shallow, and totally arguable : "guerilla" is also striking quick assaults by surprise (see China or South america history ...). So, following your logic, clan could perfectly be the side with offensive AOE and omnis those with defensive AOE - wich i'm *not* asking for, by the way : i claim equal options both side or removal of AOE in SB.
About removal, no need to argue (most people seem to agree on this).
But if you got ideas for replacement, feel free to submit.