You seem to imply that this may take a long time to run - it shouldn't take any longer to run than is necessary for the size of the trees. Or do you mean that the "side by side comaparison", would take a long time? There are visual file comaprison tools that can compare trees - if you are on a Win32 platform, I would recommend WinMerge (open source).

Personally, I would use GNU diff (available for most platforms) to do the quickest possible comparison for me...

diff --recursive --brief dir1 dir2
[download]

Believe me when I say that its very unlikely that Perl would be able to do it any quicker. There happens to be a --side-by-side option to GNU diff too!

If I still felt it necessary to get Perl involved (say, for scheduled automation), I would capture and parse the results as appropriate.