I must apologize for posting a false answer. in writing up a proof i discovered a gap which grew to a counterexample.
In fact not every sheaf of ideals of an etale structure sheaf is finitely generated. I have added a counterexample to the end of my ArXiv paper on cohomology in second order arithmetic arXiv:1207.0276v2. Intuitively, an etale ideal can hold information about arbitrarily high degree extensions which is not reducible to information about any fixed degree so the ideal is not finitely generated.
The counterexample shows that given any non-zero element $x$ of an algebraically closed field $k$ a single etale sheaf of ideals on the punctuated line $k\0$ can pick one $2n$-th root of $x$ for every $n$. The example has $x=1$ but rescaling $k\0$ takes 1 to any other $a\neq 0$.