I've had a big rotational game going over a year now and have found it pretty easy to work around. I do use MCCC to reduce culling by 95%, but even with this sometimes I still see some relationships vanish/drop lower than they should. Again though, MCCC can help as it is very easy to restore the relationship with a click or two. If you dont want to use cheats to fix relationships, the incredibly friendly reward trait and high reputation can make for fast friendships.
I'll also echo that MCCC is usually updated very fast, usually before I am home from work and for sure within a day of patches.