So after some tinkering and a days worth of mucking about in the pa_gapps_stock packages I have found a way to get the package to flash and not wipe the camera out.
Being a Convert from a LG OG and a HTC One (M7) (google edition convert) I like to use the stock apps from Google. I hate having 2 different apps for everything as well.
As with almost everyone else the PA Gapps are really the way to go.
Credit to those guys.
Get the stock gapps zip from them.
Open with you favorite falvor (WinRAR, 7ZIP, etc) We aren't extracting it.
go into the optional folder
Go to camera,,, and delete it.
Optional (not tested may work)
This will keep it from wiping out your camera but it does remove the camera app. I installed GoogleCamera from the play store and it replaced it and works just fine. Optionally you can go into the camera folder and try removing just the addons.d and lib folders.