I'm pretty sure that they have some plan/facility for pulling all of the gondolas into secure storage in the event of a hurricane strike, but a storm like the one pictured wouldn't be close to serious enough to trigger that. That was only a thunderstorm. Hurricanes, OTOH, no longer arrive in Florida without advance warning, and you can bet that there is a protocol for securing the Skyliner gondolas when that warning comes down.
In a major hurricane (Cat2 or stronger), the most serious risk is that one or more towers will go down. (And not necessarily topple over like a tree; sustained winds have been known to actually BEND similar towers that size.) The gondolas are built to be strong, but as we saw in the Canadian vandalism situation, they don't stand up very well to being dropped, which is what would happen if a tower went down. Disney won't chance having a large number of Gondolas damaged that way, so I am predicting that as many as possible will be put into storage bays in the event of a storm severe enough to close the parks. If they leave any of them on the line, they will probably be very widely spaced out. (The main storage bays behind CB are not covered, but the rails are low, so the gondolas could be secured with tie-downs, just like we would secure a boat.)