It seems to me that you have 2 options. The first is to pick a datafile format and beat both datafiles into that format, maybe using awk:
plot '<awk "-f;" "{print $1,$2}" data1' using 1:2 w lines,\
'data2' using 1:2 w lines
*Note, your awk command will almost certainly be different, this just shows how to use awk in an inline pipe.
Your second option is to use multiplot with explicit axes alignment:
set multiplot
set xdata time
set datafile sep ';' #separator for first file
set timefmt "..." #time format for first file
set lmargin at screen 0.9
set rmargin at screen 0.1
set tmargin at screen 0.9
set bmargin at screen 0.1
unset key
plot 'data1' u 1:2 w lines ls 1 nontitle
set key #The second plot command needs to add both "titles" to the legend/key.
set datafile sep ',' #separator for second file
set timefmt "..." #time format for second file
unset border
unset xtics
unset ytics
#unset other stuff that you set to prevent it from being plotted twice.
plot NaN w lines ls 1 title "title-for-plot-1", \
'data1' u 1:2 w lines ls 2 title "title-for-plot-2"
The plot NaN trick is only necessary if you want to have things show up correctly in the legend. If you're not using a legend, you can not worry about it.