We don't know how easy it'll be to craft brains usign the Scavenger. TW might still be the better way to acquire them. I'm not applying TW omicrons anymore, but I don't think they should be refunded. Not that there's a chance in hell they would be. CG rarely ever rolls back applied upgrades. Hell, some people have a the Gungan Phalanx omicron for a game mode that's about to cease to exist and CG haven't said a thing about refunding that one. Probably because they forgot it exists. The only reason it exists is that CG have given themselves a mandate to put an omicron on every single new marquee and CG wanted every Gungan to have an omicron for a different gamemode and apparently the day they were designing Phalanx's kit, they forgot that Conquest exists.
I actually like when a marquee comes out with a TW omicron. For me it basically means this character doesn't have an omicron.