Whether she should have saluted him or not, can you imagine the hullabaloo that would have been raised by the press and uneducated masses had she not done so?
The press and civvies in general don't need much of an excuse to have a go at the Armed Forces these days, so by saluting him she probably prevented a whole world of hurt being inflicted on the RAF by the tabloids.
After all, there is no rule saying you mustn't salute someone.