Bit of a breakthrough on the local research front! At the time (1683) the nearby village of Minsterley didn't have its own church and marriages, burials etc took place at Westbury (3 or 4 miles to the west). The records there contain the following entry:

1st March 1683 Anne Nicholas murdered (truculenter occisa) - burial

As far as I can tell, the latin phrase means something like 'savage death'. There are a number of baptism entries which could refer to Anne and her murderer (Francis Cooper), the most likely of which would mean he was 27 and she 23 at the time. Most interesting of all, however, is the following entry:

24th March 1683 Ichabod son of Francis Cooper, homicide, and Anne - baptism

I'm still trying to think through the implications of this but presumably it means either that Anne had already given birth when she was murdered (as opposed to just being pregnant) or that the 'Hogstow One' had fathered a child by another woman, also named Anne. Interestingly the ballad collected by Pepys (verse 8) does refer to him having kept company with "another maid beside" so who knows. I think I can at least confirm now that the original ballad is based on an historical event. If I find out any more I'll let you all know.