Another way to look at it is the hypothetical miner above processes 34 shares. If your analysis was right it would have 1 stale out of 34 even when not merged mining and thus could never have a stale rate of <3%.
And this is probably the best way to see how much "extra" merged mining is costing you.
In your status line:
SS is Stale Shares discarded (detected and not submitted so don't count as rejects)
This will show you shares that might have otherwise been valid if you were not mining merged. cgminer does not submit them so your stale rate actually will not go up as DeathAndTaxes suggested unless you enable the --submit-stale option. (I don't suggest you do).