Having not seen the programme and knowing nothing about the BBC's charter, could I ask a question? Does the Longleat branding feature in the programme? - so that the viewer is made aware that the programme is just featuring Longleat, by means of keeper uniforms, vehicle branding, reference, and the like? If it does, then surely the repeated promotion of one commercial organisation, at the (potential) expense or detriment of its competitors, is actually 'broadcast advertising'. Many of the other series mentioned here which 'promoted' such, were made by commercial broadcasters, not a nationalised one. As gentle lemur says, there should be a difference - or should there?
I'm not entirely sure what point you're trying to make here but if it's assumed the showing of branding equals "the repeated promotion of one commercial organisation, at the (potential) expense or detriment of its competitors, is actually 'broadcast advertising'" then the BBC would be able to do very little in the way of broadcasting.
Any Match Of The Day programme could be considered as the repeated promotion of Premiership football clubs over others (and lets not get into the advertising hoardings shown when matches are televised). Any series long formatted programme could be classed as advertising by your criteria -would you want all logos covered and the name of the zoo kept a mystery? As well as impractical it'd be a little absurd, especially if extended to similar "fly on the wall" programmes.
Personally, I think any positive programme on zoos (BBC or otherwise) benefits all zoos. Sure, the featured zoo may become slightly more of a destination zoo but most members of the public are still going to visit their nearest zoo (assuming it provides a positive experience) rather than traipse a long way to Longleat.
As an aside, Longleat have long been masters of promoting/pushing themselves and their advertising gets everywhere. I swear I've seen their brochures at Teebay servives on the way to Scotland and I've definitely seen their brochures in a Tourist Information Centre in Louth -over 200 miles and four and a half hours away.