this construction is simple enough that you can forget about redefining it for multiple sizes. instead, use the \text facility of amsmath:
\renewcommand{\atoi}{\text{\rotatebox[origin=c]{180}{$\iotaup$}}} this can be used both in the "main line" and in super/subscripts of any level, and it should produce the desired result.
(the definition of \text is based on \mathchoice; take a look at amstext.sty -- it isn't very long.)