This rule is not part of the \footnote command but the frame with footnotes. It's drawn with \footnoterule command within \beamer@autobreakframebox in file beamerbaseframesize.sty. When beamer computes frame dimensions it considers if frame has footnotes and draws the rule in this case.
The best solution I can provide is not draw the rule at all. Next code includes a copy of
\beamer@autobreakframebox in your file with a commented \footnoterule command. I don't know if this solution will work with other themes (I hope so).
\documentclass{beamer}
\makeatletter
\def\beamer@autobreakframebox{%
\global\setbox\beamer@splitbox=\box\voidb@x%
\ifbeamer@autobreak%
% Ok, frame was overful -> split it!
\setbox\@tempboxa=\vsplit\beamer@framebox to\beamer@autobreakfactor\textheight%
\global\setbox\beamer@splitbox=\box\beamer@framebox%
\@tempdima=\ht\beamer@splitbox%
\ifdim\@tempdima<\beamer@autobreaklastheight%
\global\beamer@autobreaklastheight=\@tempdima\relax%
\else%
\setbox\@tempboxa=\vbox{\unvbox\@tempboxa\unvbox\beamer@splitbox}%
\global\setbox\beamer@splitbox=\box\voidb@x%
\fi%
\setbox\beamer@framebox=\vbox to\textheight{\unvbox\@tempboxa%
\vskip\beamer@framebottomskipautobreak%
\ifvoid\beamer@splitbox%
\ifvoid\beamer@footins%
\else%
\begingroup
\usebeamercolor*[fg]{footnote}%
% \footnoterule%
\unvbox \beamer@footins%
\global\setbox\beamer@footins=\box\voidb@x%
\endgroup
\fi%
\fi%
\beamer@exitcode%
}%
\else%
\setbox\beamer@framebox=\vbox to\textheight{\unvbox\beamer@framebox%
\vskip\beamer@framebottomskip%
\ifvoid\beamer@footins%
\else%
\begingroup
\usebeamercolor*[fg]{footnote}%
% \footnoterule%
\unvbox \beamer@footins%
\global\setbox\beamer@footins=\box\voidb@x%
\endgroup
\fi%
\beamer@exitcode}%
\global\setbox\beamer@footins=\box\voidb@x%
\fi%
}
\makeatother
\begin{document}
\begin{frame}
\begin{itemize}[]
\item<1-> item
\item<2-> {item\footnote<2->{footnote}}
\item<3-> item
\end{itemize}
\end{frame}
\end{document}
