I think the best way is to use the add-on repositories. These are the ones compatible with Dharma (XBMC version iOS uses):
http://wiki.xbmc.org/index.php?title=Unofficial_Add-on_Repositories
Hitcher's repository is the one you want for iPlayer (the others largely worked for me).
So download the zip file and put it on ATV2 in /var/mobile.
Go to System->Add-ons->Install from zip file
and select the zip file in the home folder.
Now:
Go to System->Add-ons->Get Add-ons->Hitcher's repository->Video Add-ons->iPlayer and install.
You now have new menu (press right from Videos and choose add-ons).
Works pretty well for me.
And because it's installed through a repo, you get update notifications when available.