"In the pursuit of excellence.." sounds like a clause...and I'd be expecting a comma, followed by the second clause....like "..., Billy fell off his pogo stick." or something. You were right first time, imho.
The head seems to have caved - last time it went past the governors it was 'in pursuit of excellence'. I think it's pants to have a motto for a school anyway, it isn't some bollocks junior management training scheme. (Unless the school is Eton and the motto is in Latin. Have a vague feeling my school had a Latin motto but it had an excuse as it was created to educate girls in the days when many people thought they should sit quietly at home and do some sewing.)
Btw, cumfy, I know what you mean but to be fair, it is an outstanding school and has been for years. Not just according to Ofsted but the parents, staff and pupils, as well as other external organisations such as Investors in People (we had a review of our Gold standard recently, inspector was gushing). So I forgive the head for being a bit, um, precious about her motto - she does run an extremely good school.
I would say stick to the "in pursuit of excellence" - because without getting caught up in the technical construction of clauses, you don't need a definite article. IMHO this is because it could be viewed that there is not only one pursuit - or way in which to pursue.... ohh lordy I'll shut up before I'm off rambling again doncha love pedantry
Been suggested as a motto for an organisation with which I am involved. In the sounds wrong to me in this context. Imagine: 'Blogg's Academy - in the pursuit of excellence.' Just feels wrong but can't explain why (not that I've been out partying too much this week and my brain is sluggish or anything).