I am really sure that the fireflies are not from hitting lights directly, because Multiple Importance Sampling automatically accounts for that (unless you have lights sampling set to something other than MIS).
Also, you cannot exclude lights from GI calculation, GI is induced solely by direct lighting, you wouldnt have any GI without the lights.
So, the possible reasons for fireflies are either
- caustics (light behind some solid glass/mirror)
- bright spots (light very close to some geometry)
- general inefficiency of path tracing in interior scenes
First two causes can be easily fixed at the cost of some small bias by setting "max sample intensity" to about 5-10. The last is intristic deficiency of path tracing, I would recommend switching to PT+HD in that case.
Anyways, it would be much better, if you could post renders and screenshot of your render settings ;)