Please vote for this bug or it won't get fixed http://bugzilla.mozilla.org/show_bug.cgi?id=246560
the workaround is to click Edit> Preferences> Downloads> Plugins and untick PDF then click OK to close everything up. The next time you click on a link to a .pdf Firefox will ask what to do with it, choose to open it with acroread and check the box to always do this.
Edit - I didn't realise this bug was in Mozilla too, when I filed that bug I just filed it under Firefox. I can't see a way to fix it in Mozilla. Just taking the nppdf.so plugin away doesn't work. There should be a way to configure plugins as it's possible in Firefox.