This is really only a big issue for the formal groups and bride & groom sessions, everthing else will just carry on as normal, all be it indoors.
I visit every venue with the couple around 4 weeks before the wedding, one of the mains things I do in that time is looks for suitable places for the group shots and the Bride & Groom shots. That includes finding indoor alternatives in case of bad weather.
If there is nowhere big enough for the big groups, then I would tell the couple that in the event of having to do it inside, only smaller groups will be possible, so there is no suprises. If there is nowhere particuarly nice indoors for the couple shots, then you just have to make the best of what there is, you can't transform the inside of a run down leisure center into rolling hills and sunsets.