Here is a solution based on the redefinition of the footline, and the use of \pgfsetfillopacity{<value>}
(0=transparent, 1=opaque).
MWE
\documentclass{beamer}
\usetheme{Boadilla}
\usefonttheme{structurebold}
\usecolortheme{seagull}
\setbeamertemplate{footline}
{
\leavevmode%
\hbox{%
\pgfsetfillopacity{0}\begin{beamercolorbox}[wd=.333333\paperwidth,ht=2.25ex,dp=1ex,center]{author in head/foot}%
\usebeamerfont{author in head/foot}\pgfsetfillopacity{1}\insertshortauthor~~(\insertshortinstitute)
\end{beamercolorbox}%
\pgfsetfillopacity{0}\begin{beamercolorbox}[wd=.333333\paperwidth,ht=2.25ex,dp=1ex,center]{title in head/foot}%
\usebeamerfont{title in head/foot}\pgfsetfillopacity{1}\insertshorttitle
\end{beamercolorbox}%
\pgfsetfillopacity{0}\begin{beamercolorbox}[wd=.333333\paperwidth,ht=2.25ex,dp=1ex,right]{date in head/foot}%
\usebeamerfont{date in head/foot}\pgfsetfillopacity{1}\insertshortdate{}\hspace*{2em}
\insertframenumber{} / \inserttotalframenumber\hspace*{2ex}
\end{beamercolorbox}}%
\vskip0pt%
}
\title{Title}
\author{Author}
\institute{Institute}
\date{\today}
\begin{document}
\begin{frame}
\maketitle
\end{frame}
\end{document}
Output Obviously you will have to add your background picture but the grey bars are gone and they should be transparent!
