I think it could work, and although they've got tonnes of foot soldiers that make them seem to strong, but the direction of 'science leads' could do something for the show. I'm thinking primeval like take on it, small field team of scientists, creature experts and weapons specialists lead by Kate Stewart with the backup of troops to give the all needed re-enforcement.
Also take from the mistakes of marvel's Agents of SHIELD, it just shows a big budget show isn't always the best, and the show fails because of the bland personalities of the soldier characters who just seem to have a kill everything approach to everything, as marvel wanted a men in black sorta thing, but even in the film men in black the agents aren't deadly serious in every episode. The other thing that makes it an unsuccessful spinoff is the fact that no-one from the movies appear in the show at all, where as doctor who doesn't have A-list celebrities as the lead roles meaning it can cross over every now and again.
Finally try to make it different from Torchwood, distance the two to create two separate families of characters to distinguish the show.
So basically primeval with aliens, job done.