I think the whole point of putting Bobby in the wheelchair is so they wouldn't have to kill him - as they systematically whittle down all of the boys' allies until there's just the two of them left to fight Lucifer.

I wasn't sure about them killing off all the none Judeo-Christian gods either, but like you I thought it was good that they had at least been considered.

As for Gabriel... Well God brought Cas back to life so who knows what the future holds?