Well the Stargate programme comes under the auspices of the IOA a civillian authority. So yes the civilians are in ultimate charge of the programme.
As for the Rush vs Young, in the earlier episodes it seemed as if Rush was making the more sound judgement calls rather than Young. Sure for the most part it turned out ok in the end for Young's decisions.
From memory the catalyst for the civilians deciding to take command was Young abandoning Rush on the Planet. After all one line of thought could be 'will I be the next one who Young abandons on a planet".