Finally, I've found some time to update phpMyAdmin packages in Debian to 3.5 series. For long it was not possible due to licensing reasons, but recently this issue was resolved upstream by using jqPlot instead of Highcharts.
While packaging new version, I've also replaced all embedded libraries to use corresponding packages from Debian. I've done some testing and everything seems to work fine, but still this frightens me as some versions are slightly different than upstream.
Anyway new version is available in experimental for now. Ubuntu users can get it from phpMyAdmin PPA.