Firestorm,
There may or may not be some technicality due to the nature of the job, but certainly you could make a very very compelling argument that in everything other than name these pilots will ONLY be working for one company. Therefore they would definitely be deemed employees....that's the angle I'd pursue if I were Balpa. However, as I have previously noted, Balpa doesn't actually appear to "be" anything more than a disparate collection of CCs that represent one company only....hence the lack of representation for student pilots, newbies and smaller companies.
The fact they're employed by an agency makes absolutely no difference - or doesn't at least in IT contracting...the net result is you have one person providing services to one company = deemed employee...