Sonic Visualiser [1] can---or, at least, it makes an attempt to.
It's a highly useful tool for the analysis of music recordings.
I, too, am highly interested in the extent to which matching recordings to scores can be automated, as are a lot of music theorists. I hope you can publish a write-up of the process for syncing the audio and the score.
If there is a significant human spend required, then developing an open tool for community contributions would greatly speed up the creation of a corpus of scores.
I think a good case could be made for such an automatic system... although it's probably a somewhat too complex / labor intensive task at this particular stage for this particular project!
As for the write-up however, the process I currently use is very simple (and it's pretty much all "manual labor").
To partition a score into time intervals, I have a couple of lines of javascript that record the time the audio is at, together with where in the score I click (and where I aim to click on the note currently being played).
It doesn't take too much time and effort to partition a score this way actually, unless the piece is slightly complex. Beethoven's 5th took a little more effort than Air for example ;)
Hope this helps for now! And I am planning to publish a more detailed write up of everything, so please stay expect that in the next month or so (easiest to hear about via Twitter or by submitting your email to the site).
As for Audacity, can it recognize the beats automatically?