Really, the game should end if one side is all bots, the human team winning.
And yeh, I agree that bots should be removed from Skirmish and Pantheon. There should be an option for them in Custom Games.
For when people leave, the following suggestion sounds good.
I think the better solution would be to have some sort of "supplement system" for when people leave. So for example, you sell off all of that player's items and split the gold among the team, and then you split what their gold income would be for the rest of the team as well. This way, you don't fall behind on Citadel upgrades or anything like that, but you don't have to worry about bots winning or losing matches for your team either.