It does seem a little excessive but in the first instance, I'd check what was actually agreed. If the training hasn't started yet, it seems reasonable to check the calculation going forward.
Having undertaken the qualification myself, albeit some years ago, there is a cost to register for the course. a charge for any actual training incurred including any residential elements (if applicable) and then of course there are the hours necessary to complete the course. It's a portfolio based qualification which means the clerk needs to complete and submit work, not just attend training sessions. Some thought needs to go into whether the clerk will complete that work within his/her working hours or in addition to the normal working hours and if your clerk works for other councils, then a discussion on splitting the cost should take place.
The change to national insurance rules sadly is going to hit all but the very very smallest of parish councils as a result of a government ruling that even parish councils must comply with the change. A combination of the reduction in the threshold for paying employers national insurance and the increase in rate means smaller parishes who have not had to pay this before must now do so. Parish councils, as a local authority, cannot claim employer allowance but the government, which has confirmed that higher tier authorities are to compensated for the increase in employer national insurance, has said the compensation will not apply to town and parish councils. It's hit a lot of councils and of course their electorate quite hard.
I'd suggest a review of how that calculation has been made rather than a witch hunt about the value of the qualification if at all possible.